Your Main Base of Operations in Minecraft should be your home. Where your bed is, your chests, and anything else you might need. As such, it is a very important place, and should be treated as such. This tutorial has been divided into two parts: Beginners Necessities, Necessary Structures, and Unnecessary Structures. Naturally, Beginners Necessities are the things you need first, when you're just beginning construction of your Base of Operations. Necessary Structures are things you'll need, but are not pressing enough to need until Beginners Necessities are completed. Unnecessary Structures are things you may want simply for the fun of it.

Will add pictures and such later, once I create this stuff for myself. My plan is to do it all in survival, so that could take a while. Leave suggestions in the comments below!



Beginner's Necessities
These are things that are strongly recommended that you build after deciding where to build your Main Base of Operations. As such, they are listed in the order that I would say is best for survival. By the time you're done creating all of the things in this section, you should have a renewable food source and a mob proof Base of Operations.


Bedroom
This is the area where your bed will be. It needs to be a safe place, one well lit and organized. It should have a bed and a chest. The chest should be removed later, but for now it can stay in the Bedroom.


Walls
It is important to have walls surrounding not just your Bedroom, but any other land you want to have as part of your Main Base of Operations. As always, make sure they are mob proof, even against spiders. Otherwise, they are not effective. Make the walls simple in the beginning, and don't take an area too big for you to control. After all, you can always add on to them if you need to. It is suggested to have at least four doors, one in each of the cardinal directions.


Lighting
Now that you have walls, which usually takes multiple days, begin lighting the area inside your walls. This way, no mobs can spawn. Combine your mob proof walls with lighting, and you have a defensible area that will keep you safe. Now, you can stay up all night, and all day without having to take time off to sleep. Some would be concerned that this would let mobs spawn, but this is, in essence, an advantage. Because mobs spawn, you can get items such as gunpowder or arrows easier. Just make sure to keep any creepers you're hunting away from your walls!


Farm
Once you have a lit area, build a farm in that area. Try to keep this and other future structures ordered and in a grid pattern for ease of use. It is suggested that you make a wheat farm, as this is the easiest crop to get, and will be very valuable once you find cattle. However, if carrots are available, use those. Carrots don't require as much post-processing, and so doesn't waste your valuable time. The ideal crop is melons, since they are renewable, don't need to be replanted, and can be eaten immediately after harvesting. However, melons are extremely hard to find, so don't spend too much time on that.


Necessary Structures
These are things that you'll need, but aren't as important as Beginner's Necessities. These may easily be created in any order, and so are listed alphabetically.


Auto-Furnace
Waiting for items to be done smelting so that you can manually put in new items gets tiresome and inefficient. An Auto-Furnace would have many benefits, and a simple one can be made relatively easily.


Beacon
Once you have the resources, craft a beacon and the accompanying structure so that you'll never lose your home, and are free to explore. Additionally, it will give you perks inside your home that can help you heal quickly, get tasks done easier, and have fun jumping really high.

Cobblestone Generator
If you need large quantities of cobblestone, a Cobblestone Generator will come in handy.


Chicken Coop
Arrows are necessary for fighting blazes in the Nether, but how will you get feathers for arrows without chickens? It may be possible to farm zombie drops, but not quite so efficient as a Chicken Coop.


Crafting Plaza
For ease of use, the Crafting Plaza should be largely open, allowing you to easily get to all its components quickly. It should have a crafting table, anvil, and brewing stand. For the simple purpose of ease of use, it is suggested that the Crafting Plaza is placed near the Warehouse structure so that you can get to your supplies quickly.


Enchanting Room
An Enchanting Room has bookshelves for walls in a 5 x 5 square for maximum enchanting, and is very useful for obtaining enchanted items, which will almost certainly come in handy when fighting a boss.


Mine
Eventually, spelunking in caves and ravines just isn't going to cut it. You'll need more, and you'll need better. Therefore, a mine is a necessary structure. I strongly suggest making the layout simple and easy, for example, a branch mine is simple and easy to navigate. Don't get too ambitious, and always make sure to light the Mine.


Melon Farm
Melons and pumpkins are unique among other food resources for one simple and important reason: it is possible to make fully automatic melon or pumpkin farms. Melon Farms are, in my opinion, the best because the yields can be eaten immediately after harvest. The structure itself won't be too complex, and will give you a completely hands free and renewable food source.


Nether Portal
Like as not, there will be a time in which you desire to go to the Nether. Because of this, a Nether Portal is required. However, I would strongly urge you to not simply build a Nether Portal. Place it in a special room, one that does not have pressure plates or tripwires to open the exit doors. Otherwise, Zombie Pigmen will get into your Base of Operations; and, while Zombie Pigmen are usually not harmful, an accidental triggering of a mob attack could be disastrous.


Pasture
In the event that you need animals, be it for trading with villagers or for resources, a Pasture will become a necessity. It doesn't need to be too big, and may even be underground. Careful management of resources is required to keep your animals alive and plentiful, but the yields are important. Leather for armor, trading, or books, meat to eat, or simply to add to the scenery.


Sugarcane Farm
In order to make books, you need paper, which comes from sugarcane. You'll need to enchant items eventually to have much success in Minecraft, and so an Enchanting Room is necessary. To get this, you'll need a Sugarcane Farm.


Tree Farm
As you explore your Minecraft world, you'll find yourself in need of wood. Rather than depleting the forests around you, I suggest setting up a small Tree Farm, in which you can plant and chop down trees.


Warehouse
Establishing a place for all of your chests is important. A warehouse will do that for you. Place your chests along the walls, and keep it orderly so that you can find things easier. If possible, it's strongly suggested that you use signs to label the contents of your chests.


Unnecessary Structures
These are structures that, while unnecessary, you may find somewhat useful or fun to have around. This section is arranged in alphabetical order.


Archery Range
In order to improve your skills with a bow, you may find an Archery Range useful. It can be as complex as using pistons to create moving targets, or as simple as a block you're trying to hit. Regardless, a big downside to this is that you won't always be able to get your arrows back.


Cart Station
At some point, you may have two bases established at once. I don't know why anyone needs two bases, but hey, it takes all types to make a world, right? Anyway, if you have more than one base, a Cart Station with tracks to each base and a protected tunnel for the rails will be necessary.


Dark Room
A Dark Room is a room that is completely dark, no light sources at all. Then, with the flick of a lever (a lever is the ideal redstone output device for this structure), lights come on. The purpose of this structure is to allow mobs to spawn in a controlled environment so that they can be harvested for drops. Because of the nature of the structure, it is suggested that it is made of obsidian, with two iron doors (one at each end of a hall for exiting and entrancing) so that if mobs do blow up/somehow bypass the first door, they can't get out into your Base of Operations.


Museum
Gather as many blocks of different types as you can, and make a display for each one. It will be a testament to your hunter-gatherer abilities.


Rainbow Pens
Rainbow Pens are filled with sheep of each color. This way, you can quickly and easily breed and sheer sheep of all colors.


Roads
Some people like to be super organized and make paths. I suppose this helps them remember the layout easier. If made out of a material such as glowstone or sea lanterns, then you can get rid of some of your lighting.


Trap
If you're into hunting (real or mobs), you may find it fun to create traps around the outside of your perimeter to see which ones catch the most mobs, most effectively, etc. One upside of this is that it, if constructed right, allows you to harvest resources from the mobs, but it will also take time to gather those resources.