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Core Rooms

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 important and rare crafting materials that you don't want to accidentally lose while mining.
Mudroom
This room should 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 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, and glass. 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 to help speed up smelting since each furnace is able to run independently.
Storeroom
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 starts to overflow.
Garbage Disposal
A room in which you can safely destroy unwanted materials such as extra dirt cobblestone and sand that builds up. This could be a conveyor belt using water that leads to lava or a cacti
Entrance to your Mine
It's generally a good idea to put the entrance to your mine inside your shelter. 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 invent a decent way you can enter your shelter from the mine or vice versa without mobs being able to do the same.
Bedroom
Since Beta 1.4, 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. This room often shares purpose with another room. Also, sleeping in a bed at night causes time to pass quickly. If you want to avoid the aggressive mobs that come out at night a bed can greatly improve productivity.

Expansions

These projects, while not entirely mandatory, make your base more useful and interesting.

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 effort if you test the ideas first.
Cobblestone Generator
A cobblestone generator provides a safe and convenient way to gather cobblestone. They typically involve mixing water and lava.
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, or your spawn point is a long way from your base.
Kennel
If you have tamed a lot of wolves, a kennel is a good place to keep them in. 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 2x2 well works as well, and you can take water from any of the squares. Just don't dig it more than one square deep. You could even make the stream run downwards several stories in your building, and use it as an elevator.
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 very reccomendable to make an underground farm to avoid possible animal tampering or creepers blowing up part of your farm. See Farming.
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 no places on floor where light level is greater than 12. More about it can be found on Mushroom Farming page.
Sugarcane and Cactus Farms
Easier to manage but somewhat less useful than the above two projects, farming reeds and cactus underground requires little effort. A cactus farm requires sand to grow, and reeds need to be properly irrigated, with water within one block of it. If you don't want to spend tons of time harvesting your cactus, place a three-block-tall pillar next to where you want your cactus. Removing the bottom block allows you to place the cactus and when it grows, the two above blocks make the cactus automatically break off.
Chicken Coop
Farming eggs is possible, though time-consuming, by locking yourself in a small room and throwing enough eggs to spawn several chickens. Place water so that any eggs that are laid float toward you, and then walk away from your computer for at least a couple hours. At about one hour the chickens should have produced enough eggs for you to break even; waiting three or more hours will reliably give you a good number of eggs.
The simple "small room" method is good for starters, but it's possible to create fancy multi-level structures that drop eggs to the player as well. Hint: Chickens will always stay above water suspended by signs and ladders, but the eggs they lay will sink down. Keep in mind that, though ladders are a more efficient use of wood to hold up the water, the eggs that chickens lay might get stuck on the ladder. Using signs instead remove this potential problem.
Indoor animal farm
Light up a large area with a grass floor and you can gather wool, leather, and pork chops safely.
Example Incinerator Design
Incinerator
A room with a lava or cactus pit, for disposing of unwanted materials. 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 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.
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, but 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 four 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. If you have no diamond pick axe and cannot mine obsidian, you can create a portal by placing 10 lava source blocks in the proper places and freezing them into obsidian by pouring water next to them. Water cannot be placed in the nether, and as such you must bring 10 units of obsidian with you if you wish to build an alternate exit portal.You should build the portal 15 blocks away from your base if you don't want to hear it from there
Storeroom System
After a few days worth of play time, you will start to run out of space. Continue making more places to store your dirt and stone, or better yet, dig two blocks under the original chest and place the new chest there (you need space for it to be able to open it). You can also use signs to mark your chests. A handy place for it is next to your craft/furnace room, or on your way up or down your mine.
Mob Grinder
A safe, renewable source of gunpowder and arrows makes exploring much safer and can provide the means for large amounts of explosives.
Music Room
A room filled with note blocks to enjoy melodies made with redstone repeaters or without.

Defense

These additions make your base safer and provide a certain amount of entertainment.

Fallout Shelter
Build a basic shelter out of obsidian. This will be a place where you can retreat to in case a bunch of Creepers are out to blow you up.
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 by pulling the lever and letting the water or lava flow!
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.
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 alternitive 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.
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 XOR gate and place another switch outside your house to trigger the drawbridge from anywhere.
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. Instead, you could use obsidian too.
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.

Other Ideas

There are infinite possibilities in Minecraft. These ideas are not especially functional but can be fun to make and have.

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 to do this after building underground floors if you have a ton of resources (after mining the basement out). This could even give you a chance to "snipe" some creepers and spiders in the morning.
Remake it out of a different material.
Install luxurious violet carpeting for the bedroom. Give your craft room a nice glass roof. Rebuild the armory 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 somewhere else. 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 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, although arrows and torches will still have to be accessed from a chest or two.
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 raw cobblestone and dirt to make your buildings, and coal and iron to make tools and torches. It can require several days of gameplay to finish building.
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 the zombie and skeleton.
Lava beacon
Make a large pillar of stone or any nonflammable material and pour a lava bucket on it. It helps when you are a long way from home.
Glass floors
No mobs can spawn on glass floors, making for a handy alternative to a well-lit shelter.
Lava floors
Similar to having a lava lamp, 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
Mobs (and players!) entering your house without you knowing is a pain, that's why you need a doorbell.
Requirements: 1 Redstone , 10 wooden planks .
First craft 2 planks into a wooden pressure plate, Now take your wood and redstone and craft a note block, Place the pressure plate on your entrance and the noteblock beside it, When a mob or player steps upon the plate the note block will play a sound, You can make this more sophisticated making chimes or even a whole song that play upon entering.
Blinker Beacon
A more technical variation on the Lighthouse.
Requirements: 5 redstone , 4 sticks , 5 cobblestone (dependent upon height)
Place one block and cover each side with a redstone torch, next place redstone on top of this block, finally place a block above each torch.
This will cause a random off/on effect making the redstone torches blink, Construct this at higher altitudes so no trees or cliffs can keep it out of your sight.
When leaving the game on single player the redstone torches will turn off and no longer blink, upon relogging this may require some maintenance.
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 may 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 healing), a crafting table, a furnace and a chest. This is helpful as a simple second shelter, and the cake is a useful source of healing if you're low on health.


Dock
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 max 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 center. 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.
Library
If you have a lot of sugar cane you want to dispose of, this is ideal. You will also need a lot of wood, but in the end the library will look very cool. You can varnish the floor with red wool, and also put glowstone on the ceiling to serve as a light source. Adding in the classic secret-room-behind-a-bookcase is now possible with the inclusion of redstone and sticky pistons. Another good spot for a secret room is directly below the floor, granted the floor isn't sand or gravel.
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 drammatically cut down the time that it takes to travel vertically.
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