If you want to have base design rules, I'd suggest looking at the following:
Conspiracy X 2.0 (RPG)- a simple and clean set of ideas, though for a more gritty style campaign,
Operation Perfect Blue (RPG) - very much like running a game of X-Com UFO Enemy Unknown, perhaps a tad too involved and complicated,
X-Com UFO Enemy Unknown (Computer Game) - a classic computer game, also very good for ideas of building/running/maintaining bases, you can check it all out for free - they're making an opensource version of the game... I forget the address of the wiki right now,
X-Com GURPs (fan RPG addon) - someone wrote up a set of base design rules in GURPs a long time ago (for thrid edition... we're on fourth now), no idea where though, I recall it basically being a exact port of the X-Com stuff,
Ars Magica (RPG) - magic in the middle ages, running the covenant (home base) is a major part of the game. Writing books, inventing new spells, hiring and training grogs (the staff). The Covenants source book is nice, though probably a bit too specific to the magic setting. When building the covenant you use story hooks for certain aspects... which is nice GM fodder.
I personally like the Conspiracy X idea, it's simple and can be easily adapted to any setting and system.
Hope that is helpful, or at the very least interesting.
In fact, it might be a nice idea to do an ORE set of 'home base' rules and put them in a supplement.... (hint, hint)