Brakkart said:
Stronghold Builders Guidebook from WotC covers building castles and such. Don't think it includes rules for running domains though.
I found "Stronghold Builder's Guidebook" singularly uninspiring. It does it's job, and it does it well, but it is incredibly tedious. Better, IMO, to handwave it than to use this accountant's dream of a system.
For ruling realms and the like, the only Wizards of the Coast book that might cover it is "Power of Faerun" - I don't own it so don't know. Otherwise, I'm sure there are third-party supplements that cover this, but don't know what they are.
Stormwrack (WotC) covers all things nautical.
I found "Stormwrack" to be quite good for undersea adventures, but rather weak above the surface. I'm sure there exist third-party supplements that do this better, but again I don't know what they are. "Stormwrack" may or may not be a really good complement to one of those books, though.
Heroes of Battle (WotC) is where you go for rules on running warfare and such. That or Cry Havoc! (Malhavoc Press). I don't either book so can't say which is better.
I own both. They're very different treatments of the subject, and I find "Heroes of Battle" the superior of the two. "Cry Havoc" is a very detailed mass combat system, dealing with the control of units of troops. It's very mathematical, and left me with the exact same reaction as "Stronghold Builder's Guidebook" - better to handwave it than to get bogged down in all that stuff.
"Heroes of Battle" on the other hand, casts the PCs as a small specialist group within the main army, or as the heroic champions on the battlefield. It recasts the battlefield as the dungeon, and various enemy units as the encounters. So, the end result is that you get a scenario akin to Legolas or Gimli at Helm's Deep - they're not the leaders of the army, but rather key figures that are best used to stem the tide of the enemy where there is most need.