Freelancer MP was GOAT. Used to play on the Freelancer Universe server back in the day when it was populated (50/50 regularly) and I've never had a better time playing any game, ever. Sadly, the population has dwindled down to nothing. The sun has set, all I have now are memories. :(
Others include:
Sins of a Solar Empire (love it but I wish it were more 3D)
FTL (really enjoyed the crew/energy/module management)
Flotilla (the turn based 3D space combat is amazing)
X-Wing and Tie Fighter (yes, I'm old)
Star Ruler (the ship and station blueprints/customization of the original were out of this world)
(edit) Duskers (wasn't sure if it would count! I play with the lights out and a lit up keyboard, the atmosphere is incredible! call me old fashioned, but I really enjoy typing command strings. reminds me of DOS!)
Cheers!
