3 somewhat underrated space games that I enjoy immensely:
X3: Albion Prelude (and by extension the X series, excluding X: Rebirth): One of the greatest trader/corporation builder games I've ever played. Combat is pretty good, story is alright, and the visuals are great as well.
Nexus: The Jupiter Incident: The classic Newtonian physics fleet command game, with a pretty good story to boot. Problem is, there's a distinct lack of of a skirmish mode. Still, game is very fun.
Lastly, Sword of the Stars 2: Yes, I know, that game. Extremely bad release aside, It's a very good empire builder, and the ship designer allows a massive amount of ship flexibility. Research works in an interesting way, and battles look amazing. Although it's still a bit of a patch job, it's well worth the $20-odd price tag