You could pay adventurers to clear out the brown mold. Because mold isn't intelligent, the same solution will always work on it. Barring mutations, of course.
I agree. The biggest setting changers would be found in the Monster Manual. Giants as siege weapons would be devastating. Communication and observation via flying mounts would have an impact. Creatures with at will powers like Charm (imagine how devastating harpy units could be) could change the battlefield. Umber Hulk sappers. Doppelgänger spies. That sort of thing.
Launch trolls from catapults over castle walls. Or green slime or Brown mold.
I remember on idea I read was to use brown mold for refrigeration. This would completely change a game world. Refrigeration is possibly the single greatest invention of all time.
I don't think that would work so easily. Flying mounts would enhance communications to an extent, but unless they're much more enduring than horses, why not use mounted messengers?
Harpies could mess up battlefields, but why would the harpies serve anyone but harpies? The Daughters of Sora Kell in Eberron are powerful precisely because they
do command an army of monsters!
Creatures like umber hulks would be hard to control unless you're neogi. (In short, neogi armies would have umber hulk sappers, but they wouldn't be standard issue with [demi]human armies.)
Launching trolls from catapults would either require willing trolls (fancy that) or some powerful charm magic, and even then you'd probably only be able to capture a few. If you capture and don't charm trolls, they'll just try to get back to you.