There are several things every Minecraft shelter should have.
Craft Room
This is the single most important room and should be the first one built. A craft room should include a crafting table, at least one furnace, and at least one chest containing common crafting materials found while mining.
This room should also have supplies so you can quickly get them and leave without needing to go to the other side of your shelter to get what you need. This should be well-defended and well hidden as it's generally a main entrance to your base.
Furnace Room
This is important if you are a big miner and every miner should have one. This also enables quick production of several stacks of charcoal, smooth stone, glass, etc. Make a big room and line the walls with furnaces, possibly keeping a chest of fuel inside as well. The benefit of having multiple furnaces is a much faster smelting time for many items, since each furnace is able to run independently.
Store Room
A room full of chests for storing all of the dirt, cobblestone and other less-valuable materials that accumulates in your inventory while mining. This should be built once your main craft room's chests start to overflow. You should also build another store room directly below this one, though hiding the entrance to it, and it is the same setup as described before, though this store room is filled with more valubale and rare materials, i.e. gold, iron, redstone, etc.
Note that as of Beta 1.8, chests are transparent, and can therefore be stacked on top of each other, saving space.
Entrance to your Mine
It's generally a good idea to put the entrance to your mine inside your shelter, simply so that, if you return at night, you won't have to make a mad dash to your house. It's probably a good idea to make sure your mine is well lit, or have a decent way you can enter your shelter from the mine or vice versa without mobs being able to do the same.
Bedroom
Sleeping in a bed resets your spawn point to the last bed you slept in. Put beds in all bases to easily transfer primary bases. As an added bonus, sleeping in a bed at night causes time to pass quickly, reducing hostile mob spawning and greatly improving productivity. A bedroom often shares purpose with another room.
Brewery
Once you've been to the Nether and gathered some Blaze Rods, you can create a Brewery, which is simply a room with a Brewing Stand and a Cauldron. It is good to be able to brew some potions to prepare yourself for leaving your base. Include a chest with some potion ingredients.
Enchantment Room
After gathering some diamonds, obsidian, and sugar cane you can build an Enchantment Table. This lets you enchant your items (See Enchanting for help on design), and since bookshelves give you higher level enchantments, this room could also be a good use for your sugarcane.
Outer Walls
The best material to construct these are stone, stone brick or brick. They should be at least 4 blocks high and 2 wooden doors for the exit. Make sure to build ramparts and cover walls.
Cave Spider XP Farm
A XP farm using water currents to push cave spiders into a central area. Use a piston crusher or a long drop to get the cave spiders to 1/2 heart. Spiders can be killed by hand or with a splash potion to get XP. Note: This is more efficient with multiple cave spider spawners, as cave spiders will spawn from each spawner.
Redstone Lab
A laboratory is a large, clear, secure area where you can safely test designs without distractions. When building large projects with complicated parts, it can save you time and effort if you test the ideas first.
Cake Factory
Make a ramp farm, auto sugar cane farm, an auto egg farm, and a cow in a cage (make the cage so you can milk the cow.). Place a crafting table and a chest. Once you have enough materials from the farms, start making cakes. This is a good thing to put under/next to a dining hall in SMP.
Cobblestone Generator
A cobblestone generator provides a safe and convenient way to gather cobblestone. They typically involve mixing water and lava.
Bunker
Sometimes called a panic room, a Bunker is a small room made of strong materials (obsidian for example) with an iron door with the open/close system inside the room. This room must have a bed, a crafting table, a furnace and also a chest with the basic materials (food, tools, and weapons are a must). It also has to have a high interior luminosity to avoid monsters spawning inside.
Scout Tower
A cheap and safe way to survey the land. Note that these are mostly obsoleted by maps, should you have the resources to make them, although a map dosn't tell you if there are any aggressive mobs outside.
Beacon/Lighthouse
A tall tower with some sort of light source on the top means that you can see your base from a long distance away. Handy if you go exploring a lot, your spawn point is a long way from your base, or you have not made a bed yet.
Kennel
If you have tamed a lot of wolves, a kennel is a good place to keep them. A simple shed-like structure will suffice, but be sure to keep it well lit for the wolves' safety.
Well
A renewable water source is useful for a variety of projects. Put water in a 1x3 ditch and you can take water repeatedly from the center! For a more aesthetically pleasing pool, a 2x2x1 well works as well, and you can take water from any of the squares.
Wheat Farm/Greenhouse
A renewable source of food from the safety of your base is incredibly useful. If your base is underground or has an expansion underground it is highly recommended to make an underground farm. This will help avoid possible animal trampling or creepers blowing up part of your farm (See Farming for more information).
Melon or Pumpkin Farm
A Melon farm in your base provides a valuable food source that keeps your hunger bar up. A Pumpkin farm provides souls for Snow Golems.
Tree Farm
Producing wood in your own base can eliminate a major reason for venturing in the dangerous outside. Make sure your farming room has a torch next to each sapling and has enough space upwards. A chest with axes, saplings, and spare wood can be helpful as well. See Tree Farming.
Mushroom Farm
A big room with flat floor. You can light your farm by torches or glowstone, placed on ceiling, to prevent mobs from appearing. Just make sure that there are no places on the floor where the light level is greater than 12. More about it can be found on Mushroom Farming page. Alternatively, find a small cave or make one, put some mushrooms inside and completely seal it off without torches and check on it/clean it out. Also provides the drops from hostile mobs.
Sugarcane and Cactus Farms
Easier to manage but somewhat less useful than the above two projects, farming Sugarcane and cactus underground requires little effort. A cactus farm requires sand to grow, and Sugarcane needs to be properly irrigated with water within one block of it. If you don't want to spend lots of time harvesting your cactus, place a three-block-tall pillar next to where you want your cactus (See Farming for more info).
Chicken Coop
Farming eggs is possible, though time-consuming, by locking yourself in a small room and throwing enough eggs to spawn several chickens (see Farming for more info).
It is recommended you switch to Breeding after getting a handful of adult chickens (rather than continue to throw eggs at the wall; see below).
Indoor animal farm
Light up a large area with a grass floor. Then put two of the same kind of passive mobs (i.e., two pigs or two cows) inside. You can then breed them together and you can gather wool, leather, pork, beef and raw chicken safely. You might want to put trees inside so the animals feel more comfortable, or, if you're really ambitious, build a man-made forest.
Incinerator
A room with lava, for disposing of unwanted materials. A good way to do this is to create a two block high corridor with lava at the end, and a slab block just before the lava. This results in you being able to walk up to your incinerator but not into it, eliminating fear of death. Be careful with lava around flammable materials. You may replace the lava with a cactus block, or burning netherrack.
Obsidian Farm
Natural obsidian is dangerous to mine, let alone the difficulties associated with finding it. Make a long, narrow, enclosed pit to store lava in. The easiest way to get lava is in The Nether, so you may want a portal in this room as well. It is also possible to make redstone-to-obsidian converters. There are several examples on YouTube.
Minecart Hub
If you have active mines scattered over the place and use Minecarts to haul your stuff back to your base, dig out a universal stopping point under your base.
Indoor fishing pond
This is very easy to make, and can be very useful, especially if you don't have a wheat farm yet. Just make a hole long enough to cast your fishing rod, around 8 blocks long and at least 2 blocks deep, and fill it with water.
Portal Room
Once you have at least 10 obsidian, either from mining it in a cavern or obtaining it though obsidian farming you can build a portal. Once built, activate it with a flint and steel, and you can travel to the nether. This can be used for fast travel and for getting lava, netherrack, Soul Sand and glowstone. Beware of ghasts.
Mob Farming
A safe, renewable source of gunpowder, arrows, rotten flesh and bones. This makes exploring much safer and can provide the means for large amounts of explosives. Also see Mob Grinder.
Music Room
A room filled with note blocks to enjoy melodies. This can be made with or without redstone repeaters.
Library
Not only is it a great use for any excess sugarcane, a library can also add a bit of class to your home. Can double as an enchantment room.
Minecart Chest System
After a lot of days in Minecraft, you will soon have the ability to automate everything (farms, doors, etc). The most useful automation you can make is a Minecraft Chest System. You can simply craft Minecarts with chests, Booster rails, and some rails, you can make a system to send your ores up your mine to your base, and have a minecart with more tools come back to you.
Gravel-to-Flint room
Once you have many stacks of gravel, it can be useful to convert most (leave some for mining) of your gravel into flint. This is just a big empty room (a 4X4X4 space holds a stack of blocks), which you fill with gravel, before destroying the gravel, getting some flint in the process. It is most efficient to do this 10 - 15 times for every 20 stacks, though about 5 for 10 stacks, and 30 for 50 or so stacks. This room may include a chest with shovels, as well as ingredients and a crafting table for quick production of arrows, and flint and steel.
Lookout tower
If you always get blown up by creepers when you go out your door, you should consider adding this very handy expansion. Just make a very high platform with ladders or stairs to it, then put fences around the perimeter of your platform. This may be done by planting and stacking Huge Mushrooms. This is similar to the Scout Tower suggested above.
Target Practice Rooms (optional)
Make this room dimly lit, so hostile mobs can spawn, when you enter this room, always close the doors when entering and exiting, arm yourself and kill the mobs in there. Light the entrance area with torches. This will help you gain XP and loot.
Snowgolem Defenders
Since snowgolems shoot Mobs back, consider adding holes in the sides of your walls with little rooms attached to each hole. Then build Snow Golems behind each of the holes. You should be placing the pumpkin head 1 above the hole, because when the snowgolem is formed, it is only 2 blocks high.
Overhang
Since Spiders can climb walls, a base needs to have either a ceiling or an overhang along the outside walls to be safe. The walls must be at least four blocks high (since spiders can jump up to three blocks high). Of course, a closed roof with a lava pond on top is also nice...
Perimeter
Adding torches around your base can reduce the amount of monsters that spawn nearby, so add some light to your lawn! You can also use fences, cacti, and burning netherrack to keep enemies out. Just remember that spiders can jump your fences.
Floodgate
Using a fairly simple redstone circuit connected to a lever at one end, and one or more pistons at the other end, you'll be able to build some simple floodgates. If you extend the pistons first, and then place water, or even lava behind it, you can get rid of or even kill any mob passing by pulling the lever and letting the water or lava flow! For a quick morning mob clean-up and a strong sense of catharsis, you can place lava floodgates surrounding your entire shelter, facing out. One throw of the lever reduces the surrounding landscape to a barren, hellish wasteland! Not to be used in wooded areas.
Moat
The simplest of these is a "dry moat" or trench, a couple layers deep so that skeletons and zombies can't get across. This can provide you with a reasonably safe area that is outside. This can be filled with water to push the enemies to a mob grinder, or simply filled with lava which has more dramatic and obvious effects. Please note: It might not be a good idea to use lava when having a shelter built out flammable blocks such as wood, wool or wooden planks. Tower shelters would do well to have a three-block deep water moat to break the player's fall so they can safely fall to the bottom.
Lake
If a moat does not feel sufficient, build a lake around your base, preferably several levels below the entry level and with a bridge to allow easy access back and forth. Again, it can be water, or, if you want a dramatic flair, use lava. Remember to protect the bridge well, though, and be sure you are protected from within the island in case you miss a spawner. Making a drawbridge out of trapdoors is a fun alternative to the actual bridge.
Archery Tower
If you have a plentiful supply of arrows, building a small tower to pick off nearby monsters can be fun and provide useful resources such as gunpowder.
Dispenser Turret
Put a dispenser with some arrows at your desired location (preferably next to a door) and a Stone Button/Lever/Pressure Plate attached to it. This is handy if mobs want to pay you a visit.
Traps
If you're not satisfied with moats or a perimeter fence, consider adding a trap or two. If you're up to a challenge (and on a SMP server), you could even make an entire trap, designed to look like a base! Dark rooms with no way out for mob spawning, entire mazes made of glass, and traps using pistons and lava. The possibilities are endless.
Wall
Build a large wall, light the area inside and you can live "hostile free".
Drawbridge
Using trapdoors, some redstone, and switches, a simple drawbridge can be made. Dig a moat around your base and make sure it is too long to jump across. Now, make short walls next to your entrance. Depending on whether you have a single door or double door, you will have to use one row or two rows of trapdoors respectively. Run redstone next to the trapdoors and connect them to switches inside your base, then cover up the redstone walls. This prevents mobs from getting close to your door while you are inside your base, but the bridge will have to be left open while outside your base, otherwise you'll have to find another way back in. Alternatively, you can make a T Flip-Flop gate and place another switch outside your house to trigger the drawbridge from anywhere.
Sticky Piston Drawbridge
Sticky Piston Drawbridge, blue shows water level
It is possible to make a drawbridge using sticky pistons that is very difficult for a mob to cross. This draw bridge also involves the use of a moat or lake. A knowledge of redstone logic gates and how power is supplied to blocks is needed as this mechanism uses multiple redstone repeaters, NOT Gates and a T-Flip Flop. Using the T-Flip Flop one can wire the drawbridge so that it becomes accessible or inaccessible with the touch of a button from either side of the bridge. When the player(s) wants to cross the button is pressed causing both ends of the drawbridge and the centre to be even allowing the player(s) to cross. When activated to keep mobs out both ends of the drawbridge are raised 1 block higher than the water level making it impossible to jump from the water to dry land and the centre blocks are lowered 1 below the water level causing the centre area to flood. Assuming both areas are properly lit and secured this creates an impassable entrance to one's base.
Secure Waterfront
Because zombies and skeletons can survive sunlight in water and hostile mobs can swim, if you have a base on the coast it's a good idea to make sure it isn't vulnerable to mob attack. Building canals, lighting nearby islands, and building walls on areas of water you don't use can stop very rare, but still as deadly, attacks from the sea.
Blast shield
About 3 or 4 layers of some cheap material (e.g. dirt) placed on the house will make it ugly, but it prevents creepers from doing any damage to your house. Alternatively, you could use 1 layer of obsidian instead.
Self-Rebuilding Wall
It's possible to apply the idea of a cobblestone generator and use pistons to make it automatically rebuild damaged walls. Generally more effort than it's worth, but very neat-looking.
Land Mines
If you like to blow up stuff, you might like this. All you need is a lot of pressure plates (wood) and TNT. Once you found your spot dig two blocks down. Then place the TNT then another block, then the place the pressure plate. You can have a big mine field but usually more effort than it's worth.
TNT Cannon
TNT cannons are a good destructive way to take out mobs. Make a TNT cannon and have a chest full of TNT. For more detail go to Tutorials/TNT Cannons.
Iron Golem Trap
If you have the latstet 1.2 snapshot, you can create a seperate room containing multiple iron golems. This can be opened via a piston door to allow iron golems into a courtyard or garden. This will allow them to be sent to kill zombies if your house is under siege
Cactus Wall
If you have a small house near or in the desert, and you want some more protection because your just starting out, or if your a veteran and you want a cheap, efective wall, then this is the wall for you. It's basicly composed of cactus blocks, placed about 3 blocks high, and all around your base in a way like this:
o o o o o o o o
and only make one path to your door, this will trip up most mobs, other then skeletons because they shoot, and spiders, and they tend to jump over it, but it's an excelent defence for a beginer.
Add underground floors to your shelter.
Using this gives you a chance to find resources, and, in the case of invasion by mobs, it will always provide a safer spot. Underground floors are also useful for making mob grinders or animal farms.
Add above-ground floors to your shelter.
It is normally advised that you do this after building underground floors, especially if you have a ton of resources (after mining the basement out). These floors could even give you a chance to "snipe" some creepers and spiders in the morning.
Balcony
Place your balcony where it is facing a nice view! Add a chest with bows and arrows for quick mob sniping.
Remake it out of a different material
Install luxurious violet carpeting for the bedroom. Give your craft room a nice glass roof. Rebuild the armoury out of obsidian. Redo your outer walls in smooth stone. Add a second story to your library.
Make another base in a new location
Having more than one base helps if you need to travel farther to get resources. A base next to your spawn point is helpful if you built your main base far away and you died at night. A base in a desert can provide sand, and a base in a tundra can provide snow. A base hovering in the sky can provide entertainment, especially if mobs spawn on the edge of it.
An emergency kit
In case you need to quickly gear up and run back to get dropped gear. Perhaps a sword, cake or a stack of porkchops, a stack of torches, and maybe some TNT? A more advanced kit can be made from dispensers that give you items at the click of a button or a step on a pressure plate, although arrows and torches will still have to be accessed from a chest or two (if you want the whole stack).
Add an escape tunnel
You never know, that creeper might one day get you. Bonus points if the tunnel leads to a secondary base.
Lava lamp
Simply make a hollow space out of glass and fill it with lava. An efficient method is to run a vertical column through many floors powered by a single lava block at the top. You can also make one of these high above your base to mark it from afar. If your house is made out of flammable blocks, this isn't recommended.
Quarry
A Quarry yields very large amounts of materials such as cobblestone and dirt to make your buildings, and coal and iron to make tools and torches. It can require several days of game-play to finish building. Some rarer materials like gold can be found as well.
Mining shaft sunroof
Making a sunroof that points directly down your mining shaft has its advantages: you will be able to tell the time of day more easily, and burn mobs like zombies and skeletons. The sunroof can also provide enough light to discourage other mobs from spawning in your mine.
Lava beacon
Make a large pillar of stone or any non-flammable material and pour a lava bucket on it. It helps when you are a long way from home. Make sure not to build it too close to your base if it's made out of a flammable material.
Glass/lava floors
No mobs can spawn on glass floors, making for a handy alternative to a well-lit shelter. Light is still important, though - you could even have a 1 block high space below all glass blocks on the floor and pour lava there. This will keep your shelter visible and provide a fancy, creepy feel.
Doorbell
Players (and mobs) entering your house without your knowledge is a pain, that's why you need a doorbell. When a mob or player steps on the pressure plate the note block will play a sound, and you can make this more sophisticated making chimes or even a whole song that play upon entering.
If you have multiple entrances to your base, place different blocks under each note block to make sure that if a creeper comes to your west entrance, you don't get blown up when you try to run away through that door.
Blinker Beacon
A more technical variation on the Lighthouse - the light blinks on and off like a real lighthouse.
You may also use a minecart rail system, which can be made so you put down rails in a square(4 rails on every side), then put down a booster and detector rail, power the booster, and connect the detector rail to the torches you want to blink with redstone. Place a minecart on the booster and it will loop forever.
This can be used to blink multiple torches with the same system, and does not require maintenance. You can connect more detector rails for faster blinking speed.
Outpost
Make a small room somewhere away from your base. You can include a bed, a cake on a table (for food), a crafting table, a furnace and a chest. This is helpful as a simple second shelter, and the cake is a useful source for restoring the hunger-bar if it gets low. Add a door and windows to know when that creeper is staking out your door.
Dock/Harbor
If you find yourself using boats in a general area often, making a dock or two is a good idea. They can help prevent your boats from drifting off into the ocean, or slamming into a wall when you exit, thus breaking the boat. Dispensers can also be placed here and filled with boats for convenience. Chests filled with boats are a good idea too. There are several ways to make useful docks.
Placing half-blocks in the water. When a boat moves on top, it will slow down and stop immediately. Half blocks are shorter, so your boat will not collide with it and break.
Warning: it is recommended to only use this method on Peaceful difficulty and to land on the half blocks at a low speed, instant death is possible when landing on half blocks at maximum speed.
A closed dock. One type of dock is by making a small area (2x3 or larger) that is filled with water. You can place doors in the water, allowing you to ensure your boat will not drift off. Soul Sand is a suggested building material, as it will prevent all of the impact damage from colliding with a wall made out of it.
Water currents. By using a bucket to remove the top layer in 2+ deep water, you will create a + shaped water current flowing towards the centre. You can use this to hold boats, while still being able to escape somewhat easily. This design does not always prevent the boats from moving if you or a mob bumps into it, but will help prevent it from drifting away
Piston elevator
If your base happens to be atop a large mountain or if you have a deep mine below you base then a elevator may be a good idea. Elevators dramatically cut down the time that it takes to travel vertically.
Fridge
Create a fridge by placing a dispenser on the ground, a block on it and a button on the side of the block to quickly get something to eat when you're starved. Add a door in front of the dispenser if you feel it would look better, or if you just like the idea.
Miniature zen garden
Either above the surface or underground, create decorative minimalistic works of art using water currents, plants/crops/flowers, sand, clever use of fenceposts, signs, torches, etc.
Fountain
You need 22 stone and a bucket of water. Make a 5 by 5 square with the nine in the middle taken out so the water won't spill, then make a 4 block high pillar in the middle and place the water on top of the highest block. Taking out the stone pillar in the middle of the fountain can look nice, and placing half-blocks around the stone blocks can look fairly cool.
Piston Doors
These are very cool looking. Have these anywhere in you house: library, craft room, furnace room, you name it. All you need is redstone, sticky pistons, and levers. Be sure to keep them hidden if the rooms are secret.
Tunnel to a Stronghold
After you found a stronghold make a tunnel to it. Easy way to get to The End. Keep it well lit and defended so that the creeper you ran into in the stronghold can't follow you back to your base and blow up.
Add a carpet
You can spice up your base by adding a carpet made out of colored wool. Make sure that fire and lava aren't less than two blocks from the carpet otherwise, well, your carpet will go up in flames! Bright colors, like red, blue and purple are recommended, because black and gray carpet don't have the same feel.
Roller Coaster
If you have enough resources, build a roller coaster out of rails. This is a decent way to keep occupied while you have nothing else to do in the vast world of Minecraft. Useful on SMP- you can charge other players to ride.
Sky Base
Create a base floating in the sky with no bridges or stairs connecting it to land. Of course, it doesn't have to be this way to build it! The no-connections idea can be accomplished with waterfalls, piston elevators, and nether portals. Add other sky islands nearby with bridges to connect them, and it'll be like you never left the ground!
Battle Arena
The first thing you must do is find a mob spawner. Then seal off any extra entrances and place a door at the last remaining one. Maybe make the dungeon a little bigger, to provide for more fun. Finally, make a lobby room with chests full of equipment (swords, bows and arrows), potions and food. Now you can fight that specific mob whether for experience or drops for as long as you want! Include beds if it is a long way away from your base, so that if you die you won't have to walk for ages just to find it again.
Railway
Make a long tunnel to fit from one to any amount of minecarts, then use minecarts with furnaces to propel the 'train'. You can also use powered rails, but for that you'll have to find gold and redstone. Be sure to add emergency chests to the side of the track and fill them with coal to power your minecart so you don't get stranded. Adding food and weapons in these chests is a good idea, in case you get stranded and have to fight some zombies to make it to your shelter. This is fun for SMP and single-player and you can go across the land quickly. Don't make your railway aboveground; you will constantly be attacked by creepers. However, covering the railway with blocks (such as you would make a house) can solve this problem. Make stations for your favourite landmarks (big mountains, your house, etc).
Minehouse
Make one of these if you have a mine and have to constantly run up and down a long tunnel to drop off your bounty and sleep for the night. You need to make a small cottage in the middle of your mine. It must have a chest with food, picks, and shovels. A crafting table, multiple furnaces for quickly smelting items, and a bed are always good to have inside. You can also include an Enchantment Table.
Pool
Make a 5x5 (optional) hole that's 2 (optional) blocks deep. Fill it with water. And now you've got your very own pool. And if your extra careful, you can make it with lava instead. Also it lights up that area of your base and looks good.
Park Square
Make fences around a 20x50x15 area, put a garden, and a wool statue with a stone base.
Work Tents
If you feel that you're running out of inventory space frequently during above ground projects, build a work tent. Make a 4x4 fence box, add a door and wooden roof, and place lots of chests. Add a least 1 furnace and a workbench. Dig a little ditch in case a skeleton or spider appears. This can double as a safe-house/tent.
Mining Rig
Create a platform on top of a relatively flat surface or mountain. Dig out a trench in the middle of it and place redstone on either side connect the redstone to a single button and fill the trench with TNT. All you need to do is to press the button and you will begin a pit that leads to the bottom of the world. A automatic reloader can be added via sand and pistons.(Can be easily repurposed into a cannon)
source : minecraftwikia
