Dog Moon said:
How do I go from refugees to recognized leaders? How do I make it interesting instead of someone finding them, seeing that they're better than the others and skilled in combat and use them for minor missions until giving them forces of their own? Heck, I'm completely at a loss atm of what missions would be good to start off...
One thing that refugees might have going for them is that they are (perhaps) unrecognizable to the enemy. That means they'd make good scouts/spies.
Most PCs (of good alignment) will intervene if they see something obviously evil attacking, and overpowering something good. So if a lone deep gnome is set upon by a few low-level drow, the PCs can save them. That lone gnome might be an advisor to one of the higher-ups in the city, and so in a position to recommend the PCs for a spying mission.
Rather than spy within the stronghold of the enemy, they could spy on an outpost. They
think they're just going to collect information and return, but in the course of spying they see something that intrigues them and/or forces them to intervene - perhaps a long-lost friend from their old town being held hostage, or maybe a chance to steal/break/take something important.
Or maybe they are following another spy to a city that's "neutral" in the conflict. A "neutral" city could be hard to come up with. I suppose you're running this in a standard Underdark environment? In that case "city" could be replaced with a Mercane trading post, Myconid colony, or whatever. Scouts have followed some agents of the enemy to this place - no doubt they plan on buying some obscure magic item to help them with a phase of the war. Perhaps PCs could use diplomacy to get the myconid/mercane to not deal with the enemy. Of course they get bonuses to diplomacy if they first undertake a mission on behalf of the traders...
Also - perhaps a fellow refugee is really a turncoat for the enemy. The PCs, being from the same hometown, are in a unique position to overhear the turncoat talking to agents of the enemy, and intervene.