Oh boy, you don't know what you've got yourself (and me) into...
Right, the Combine are going down at some point. Despite the multiple universes thing they are being raped by a physicist. So, not them.
When you say "Zerg" I'm going to lump them in with Tyrannids from 40k cause they are essentially the damn same. I don't know what happens with the Zerg, presumably not much since StarCraft is balance to a tee, and 40k's Tyrannids are pretty much consuming every planet they come across. These guys are contenders.
Imperium of Man: for all the fact that they are badass marines in suits their empire is falling and will at some point, I don't fancy their chances.
Hell: I guess so, maybe. However in theory God could take them out at any time otherwise he loses the omnipotence thing.So I still reckon Zerg/'nids.
Galactic Empire: they were taken out by rebels from their own galaxy. Sorry, but they are down and out. Unless they have Luke who becomes Godlike in the extended Universe, then I'd give them a chance.