If you're willing to go the Pathfinder route:
Pathfinder Adventure Path #32: Rivers Run Red (Kingmaker 2 of 6) is largely compatible with 3.5 and contains:
Expansive new rules for running your own cities and nations, by James Jacobs.
These are going to be expanded upon in Ultimate Campaign, a recently announced 2013 source book which will contain rules for:
...building building strongholds, attracting followers, and conquering kingdoms through warfare or guile...guile…
