Two books you might want try and track down are 3.0's "Stronghold Builder's Guidebook" and Pathfinder's "Ultimate Campaign". The Stronghold's building formula is a huge mess and everything is feel fairly expensive though the
Landlord feat presented on page 10-11, really helps with the costs. On the flip side, the shear amount of customization the Stronghold Builder's Guidebook allow is nearly overwhelming. The Ultimate Campaign on the other hand, is significantly less varied, however, the rules for construction are simplistic and cheaper (and it provides the listed benefit for each piece). In addition, Pathfinder presents two ways to pay for a building pieces, either with gold or the [goods, influence, labor, magic] system introduced in the same book. You can check out a chunk of relevant parts of Ultimate Campaign
here.
I've use both books in various campaigns as both a DM and a player. From my experience, I would use the Ultimate Campaign's building method as the baseline, while utilizing the Stronghold Builder's for ideas, the various magic items listed as well as a guideline for "fancier", unlisted, and/or impossible (floating mage's tower anyone?) building pieces. If you do this and allow someone to take the Landlord feat, you will need to either scale back the amount of gold provided or restrict it only being used for things within the Stronghold Builder's Guidebook.
Slightly off topic, but I've also found that Leadership is a must for making large scaled bases.