Bases are the most important asset that a commander of X-COM can possess. Bases are where extra weapons, ammunition and armor are stored for your troops. It's also where captured aliens and artifacts recovered from crashed UFOs are researched to allow new and deadly forms of warfare. It's where ships that were damaged in the battles with the alien space ships are repaired and equipped. It is also where you construct monstrous ships of awe-inspiring power and create armor of startling strength.
The bases in Apocalypse have predefined areas where it is possible to build new facilities, all linked by corridors. It is impossible 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 randomly selected base, and if needed, the Government can be contacted to give additional base(s), provided the funds are available. The layout of those new bases can vary, so it is prudent to examine the layouts before making the purchase.
Buying A New Base
There are 4 factors to consider when buying a new base: Cost, Layout, Building Type and Location. A complete list of all the buildings and their characteristics can be found at Base Locations and a detailed analysis of their layouts at Base Layouts.
Another important factor when buying a new base is the number of aircraft launch tubes present at the building. The more it has, the faster multiple X-COM craft can scramble to intercept enemy craft, although this can also be achieved by parking aircraft into the buildings of other Organizations, especially the Space Port.
Base Location and Type
Since X-COM will mostly be employing air vehicles the location of the base or number of launch tubes isn't that important since aircraft can be strategically docked anywhere in the city, allowing them quick access to any part of Mega-Primus.
Warehouse exteriors can sustain more damage than Slums and their lower profiles make it harder for stray shots to hit them.
Slums cost about the same as Warehouses but the structural integrity of these badly maintained buildings is questionable. They are much larger targets and crumble easily. In addition to that, any building connected to the slum will collapse with it.
Slums are usually the only kind of buildings purchasable in the more remote and dilapidated areas of the city.
With either type of building, if the main square where the agents and vehicles are stored is hit and it falls down, agents will get killed and craft will be destroyed. This risk is greater with slums.
The type of building will also affect where you fight if you choose to investigate your own base when aliens have infiltrated the building but no base attack has commenced.
There a many considerations and trade-offs to make when planning your bases. Base location, security, coordinating human resources, etc.
Bases with large layouts are able to have more facilities constructed in them, and can make good all-purpose bases. Bases with limited space need to be specialized as a specific type of base, such as one which only repairs your vehicles, researches Quantum Physics/Biochemistry or only contains Workshops.
Every base needs a few Living Quarters and a Stores module. If a base is attacked by an organization, it is necessary to have at least one agent at the base otherwise the base will be destroyed without opposition. In addition, any Workshops will require at least one storage module to store the newly manufactured items.
It is a good idea to cordon off the entry points with Security Stations. With the stations in place, enemy forces will often suffer heavy casualties before defending agents run into them. In case the stations fall, they will have damaged the enemy force considerably or at least delayed the enemy long enough for you to lead your scientists to safety and coordinate your combat troops.
One consideration for managing raids is the distribution of personnel at the base. In combat, you have six squads of six agent slots that is shared by your agents and the technical staff. Six of the individual slots are reserved slots (for mind controlled units and presumably the security stations), leaving room for only 30 personnel to appear in the battle. In an overcrowded situation where you have a lot of agents and technical staff, you will have no choice in which agents or how many of them appear in the battle once the raid commences.
On a similar note about staff distribution, if all the scientists, engineers and agents are present in one base, it is very likely that one well-placed attack on the building may completely annihilate the entire platoon of agents and technical personnel. For this to happen a piece of building needs to fall on top of the bay through which X-COM agents enter and leave via car. To reduce the risk of such a catastrophic loss, either avoid using Slums for research or manufacture complexes, or consider decentralizing the labs and workshops to smaller bases around the city.