Interesting question. I haven't really dealt with this issue in my own games, but I'll venture an off the cuff answer.
I think there are two very distinct aspects to being a good general and history is riddled with examples of generals who were good at one or the other, neither or both. There is the ability to inspire men to fight and to lead them into battle. This is clearly Charisma based and I'd probably use Diplomacy as analogous or (if it were a reluctant army of Goblins or Orcs) perhaps Intimidation.
Distinct from that is the matter of strategy and logistics and this seems to be clearly a matter of Intelligence. I'd say that Knowledge: Strategy might fit the bill. Alternately, I'd venture that Appraise would address a lot of the logistics issues, if not the strategic ones.
That doesn't address the problem of Fighters (who would seem to make good Generals) not having Knowledge as a Class Skill. Sorry.
Yeah, we're basically going with a Knowledge skill, but I wanted to see if there was anything in "da r00lz".
I don't have a problem with fighters not having this as a class skill. There are feats-a-plenty that would cover taking a knowlege skill as a class skill and some of the best generals have been poor combattants.
The feat gives you some followers to order around, but how good are you? Does a INT 5 Fighter with the Leadership suddenly become a fantastic leader? No. But a INT 5 (or INT 12) Fighter with ranks in Knowledge(Warfare) would make a better leader in the Arts of War
As a previous poster speculated, in Sword & Fist, p. 10, under "New Knowledge Skills", there is the following:
- War (siege engines, sapping, siege tactics and strategy).
I'll also point out that the Warmaster prestige class (S&F p. 37) requires the Leadership feat and 5 ranks Diplomacy, so perhaps those are apropos on the "inspiring troops" side.