Bases (Apocalypse)
Bases are the most important asset that you, as commander of X-COM, could ever possess. Bases are where you store your extra weapons and armor for your troops. It's where you store your ammunition, your captured aliens, your artifacts that you stole from the alien's ships and carcasses. It's where you fix those ships that were damaged in the battles with the alien space ships, and where you research these new and deadly forms of warfare. It is also where you construct monstrous ships of awe-inspiring power and create armor of startling strength.
Base Layout
The bases on Apocalypse have predefined areas where it is possible to build new facilities, all linked by corridors. It is impossible however to expand the base more than the already excavated areas, which can limit the usefulness of a base.
The game starts with X-COM already in possession of a base, and if needed, the Government can be contacted to give additional base(s), provided the funds are at your disposal. The layout of those new bases can vary, so it is wise to check the bases available before purchasing a new base building.
Buying A New Base
Another important factor when buying a new base is the number of launch tubes for aircraft that the building possesses. The more it has, the faster multiple X-COM craft will scramble to intercept any UFO or hostile craft, although this can also be achieved by placing craft into the buildings of other Organizations, especially the Space Port.
Base Location and Type
Since you will be using mostly air vehicles it doesn't really matter the location of the base since aircraft can reach quickly any part of Mega-Primus.
More important is the type of building where the base is located. All bases are either Warehouses or Slums. While this has no effect during Base Defense missions since they will be fought using the base layout, it can be of extreme importance during the Cityscape Fighting.
Warehouses are more tougher than Slums when taking a hit from craft weapons and their profile is lower, making them harder to be hit by a stray shot. Slums usually cost less (depending on the base layout) but the structural integrity of these badly undermaintained structures is very questionable. If the square containing the craft/agents is hit and it falls down all of the agents present at that base will be killed, and any craft present will be destroyed.
Base Design
Bases with large layouts are able to have more items constructed in them, and can make good all-purpose bases. Bases with limited or contorted space needs to be specialized as a specific type of base, such as one which only repairs your vehicles, or only researches Quantum Physics or Biochemistry, or only contains Workshops. Don't neglect to put in a few Living Quarters and a Stores module, though. If you are ever attacked by an organization, you need to have at least 1 soldier at the base otherwise your opponents will destroy the base without opposition. Also, if you are investing on Workshops, you should be aware that you will need storage modules in order to store the items which you just manufactured.
When planning your base, it should be noted that Vehicle Bays and Access Lifts are able to be infiltrated by hostile forces. If your bases ever come under attack, these are the areas where the enemy will most likely enter from. To counter this, I usually cordon off these sections with a small string of Security Stations, be they the advanced or regular form. This usually means that the enemy is shredded before you even run into them, and, in case your defenses fall, you can be certain that they enemy will be down most of its assault force.
Finally remember that you can transfer people between bases. If you stick all your scientists and men in one base, it is very likely that one well-placed missile or beam can completely annihilate your entire platoon of troops and all your researchers, which would be a catastrophe. Also, you will only lose the men in your base if a piece of building falls on top of the bay through which your men enter and leave via car. Otherwise, the aliens can destroy your entire base and you'll be fine.