Cry Havoc's another OGL fantasy mass combat system, put out by Malhavoc Press some years ago. A cut-down version of it also made it into the Advanced Player's Manual, from Green Ronin.
Oh, and there's Warfare for Beginners, by Morrus, the guy who runs this show.

It's like, half a dozen pages or so, and looks pretty neat. Haven't put it to use so far, but still, worth a look.
There were one or two netbooks, from the early days of d20, that dealt with this stuff too. Dunno what they're like, but well, they're also free.
Anyway, just a few that haven't been mentioned so far, so's you can get closer to checking out the whole range that's out there.
There are many systems that can be grafted onto d20 fantasy for domain management and the like, but it's really very much taste-dependent.