Depends what your looking for exactly.
Sins or a Solar Empire (get the collected edition), Master of Orion (1 and 2) and Galatic Civilisations (2's the best) are 4x rts set in space.
FreeSpace 2, Freelancer and Star Lancer are space sims focusing on you piloting a single craft and more dogfighting based with varying levels of exploration and trade (well in freelancer at least, the other two are straight up fleet level combat.)- best enjoyed with a joystick.
X3TC, or Terran Conflict X3 is a more interesting beast. You are again an individual but you have the oppurtunity to really live in the game universe. You can hunt bounteis in rouge systems, join one of the factions, create a mercantile empire, build up your fleet of battleships to crush or enemy or do pretty much whatever you want.
In one of my files for example i have built up a corporation based on mining and energy production and with huge profits created a massive fleet with which i invaded one of the factions (the parranid just annoy me) and then another faction joined in the conflict.
Personally i think X3TC is the best 'space simulator' stlye game as it combines trading, exploration, combat and gives you strategic rts elements as well as rpg elements. It also has a thriving online community and forums to get help from. It is also relativley recent and as such has very pretty graphics.
Freespace two is great for some spacecombat from a fighter sized ship and can become very enjoyable. The other good thing about these space sims is that theri cheap. X3 is about $15, Freespace 5, the others in the same range (from digital distributors).
Space sims in general though can take a while to get into and can have pretty steep learinging curves while you learn the often very large no. of keyboard controls. (not so much for the rts ones though of course)
Edit- Remembered some more
Homeworld 2, another rts set in space. Hegemonia again space rts. The AI war series- you design ships and fleets and then send them into battle. Nexus the Jupiter incident another rts and Star Control 2- action adventure genre. If your looking for 'typical/traditional' rts' then Homeworld and Nexus are your best bet, Sins and the others are 4x's. There are a lot of indie games out there too, such as star ruler (can build your own ships! and a truly awesome scale, you can build a deathstar as large as a galaxy if you really wanted to and had the time) try looking through steam or impulse for some.