I have one production base with a factory, 310 runts and 10 defenders, one hangar, the rest is dedicated to production, living and defence. I might sell the vaults at some point if I have enough slave, my 2nd base (the one with the large prison...) has negative storage at the moment. The one that was supposed to be my production base was razed by the church, so I redesigned another one (base 6)
2nd base is a production base as well, but not as focused. 100 runts. Also has the mentioned prison and a larger garrison because I used to have a convoi of mostly slave soldiers there. Some brainers here as well.
3rd base is an interceptor base and they house my underwater team. No production capabilities at all.
4th is my training base, and because those guys bring stuff back it also has around 60-70 runts who do something with it. Space for 13 brainers as well, but I fired them when I hit a bottleneck. Probably wont rehire them, main base and 2nd base is enough.
5th still has a few plantations for the times I need sectoweed, but they get upgraded with more interceptors at the moment.
7th is an interceptor base, and as I recently unlocked mansions (late in 2603 ... one might come to the conclusion that I don't like the mission) I decided to build up an infiltration squad here. They can try terminal terror as well then, the first one was a desaster.
8th ... well ... I haven't rebuilt so far, but if I do it'll either be a second factory to churn out more tanks or another interceptor base (it will be in antarctica).
Some hangars are used for ships I am reluctant to sell, like the Prospector that will serve as the infiltration teams ship (probably) and a convoy that I sometimes use to keep something on the map until a more convenient time.
Building my 1st Sabre at the moment and thinking about the Leviathan, but I barely get the Thunderhorse full, and the Leviathan is slow.