I discovered a squad builder site recently and was a little giddy. I love it, but read some things that there are many out there. I am using:

http://jediwars.com/game/SquadBuilder

Are there better ones? I didn't think it could get better, but I figured it is worth asking!

http://ia-armies.com/

while not as flashy, i like it a lot more, esp for the command cards

I second ia-armies. I have used it primarily at work during my lunch to think about possible combinations for my next skirmish battle.

I like the jediwars one as well. I've used both. Each have their pluses and minuses. I do like the full card art on JW though. Doesn't have the new wookies, stormies, guns cards, yet. But I'm sure he'll get them up soon enough. His the says he's working on a printable option.