GW's BFG is pretty good. I have many fleets from that game. There's also Ground Zero Games' Full Thrust (and supplement More Thrust). If you want simple, though, you might want to check out Wizard's Star Wars Miniature Battles and the rules in the Star Wars Saga RPG. It treats starship (and air/ground vehicle) combat like character combat. Not the most realistic simulation of space combat ever but definitely a simple enough system to include in a RPG. Not saying to copy it, just that you might want something similar. Of course you could go the other direction and do something like Harpoon in space Kill me first, though, because I'll be forced to buy it and then I'll hate myself later because I just can't wrap my head around the rules.
M