Star Wars: Rebellion (as much as most hate it, I absolutely LOVE it)
Star Wars: Empires at War (ground battles suck, but large space battles are pretty epic and what I always imagine an updated Rebellion would be like)
Freelancer (loved it, though was disappointed that it didn't do much to expand on the Starlancer plot)
Imperium Galactica 2 (loved the game, but it eventually got to a point where it got boring once you built 50 battleships and overran everything)
Sins of the Solar Empire (I feel like I'm the only person to absolutely hate this game with a passion)
Maelstrom (NOT the 1993 Asteroids clone, nor the 2007 version)