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Core Rooms

There are several things every Minecraft shelter should have.

A 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.
A 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.
A 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.
The 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.
A Bedroom
Since Beta 1.4, sleeping in a bed resets your spawn point to the bed. 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.

A Cobblestone Generator
A cobblestone generator provides an extremely safe way to gather cobblestone, to learn how to make a rather bulky but very efficient cobblestone generator, click here.
A 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.
A Wheat Farm/Greenhouse
A renewable source of food from the safety of your base is incredibly useful. See Farming.
A great tutorial on how to make a greenhouse can be seen here.
A 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 at least 5 free blocks upwards. A chest with axes, saplings, and spare wood can be helpful as well. See Tree Farming.
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.
You can view a video on how to make a cool looking and effective reed farm here.
Tree House
Unless your house is a tree house, it is useful to make one as a second base. Bonus points if they are close together
Many more bases
Build many bases and houses in many different areas like a base above water, a base below water, a base on the side of a hill or mountain, and a free standing fort.
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.
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
An Incinerator
A room with a lava or cactus pit, for disposing of unwanted materials. Be careful with lava around flammable materials.
View this video to see how to make your very own incinerator
An 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 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 use temporary obsidian farms to build a portal anyway. Having a portal adds a very small chance of ghasts spawning outside of the nether. You can change this by disabling your portals when you are not using them.

Defense

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

An Overhang
Since spiders can climb walls, a base needs to have either a ceiling or an overhang along the outside walls to be safe. Of course, a closed roof with a lava pond on top is also nice...
A 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, cactus, and burning netherrack to keep enemies out.
A 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.
A 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.
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.
A 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"
Mix and match
Feel free to use many if not all of these ideas to build the ultimate defence, use your imagination that's what minecraft is good for.
Drawbridge
Using hatches, 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 hatches respectively. Run redstone next to the hatches 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.
Secure any waterfronts
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.

Other Ideas

There are infinite possibilities in Minecraft.

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.
Add above-ground floors to your shelter.
It is normally advised to do this after building underground floors if you have a lack of resources. 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.
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?
Add an escape tunnel.
You never know, that creeper might one day get you. Bonus points if the tunnel leads to your secondary base.
Make a panic room/bunker.
Make a small saferoom out of obsidian. Set up TNT in other areas that can be detonated from inside!
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.
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.
Mob Grinder
A safe, renewable source of gunpowder and arrows makes exploring much safer and can provide the means for large amounts of explosives.
Animal Farm
An animal farm in/under your shelter can give lots of passive mob drops.
Quarry
A Quarry yields very large amounts of materials such as raw cobblestone to make your buildings. It can require several days of gameplay.
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 , 11 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
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.
Boom Sequence
Rebuild your house out of TNT and set it off. Very useful if you're bored. Making a backup of your world is suggested.
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. There are several ways to make these.

- 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.

- 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 torwards 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.

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