TIE Fighter was awesome, yes, I have to give much love there, but as much as it hurts me to say it, I have to give the edge to Freespace 2. The original was brilliant as well, but Freespace 2 took everything to an entirely new level: gripping story, great enemies, mind-boggling capital ships, truly stunning graphics, and even a fantastic ending. I can't think of a single thing that game did that it didn't do well. It still hurts that there was never another sequel.
And because I can't help myself, honourable mentions:
Homeworld: I hate RTSs, I love Homeworld. Everytime the whole "are games art?" debate flares up, I want to pull my box off the shelf and throw it at someone. It wasn't even a great RTS; the AI was pretty half-assed and easily exploited, which meant that some of the near-end-game battles were actually remarkably simple, and put you in a position where your fleet was an absolutely unstoppable juggernaut. But the package that RTS was wrapped in was simply awe-inspiring. (Homeworld 2, however, was shit.)
Mechwarrior 2: A bit borderline, since you weren't actually fighting in space (except for a single combat in Ghost Bear's Legacy), but you did travel between planets and fight on behalf of grasping interstellar empires, so I'm counting it. Great combat, awesome soundtrack, and I had an absolute blast playing online in the Netmech Registry.
Wing Commander: Primitive now, but in its day it was revolutionary. There are two kinds of gamers in the world, those who played WC, and those who did not. If you didn't, don't bother; dig up TIE or FS2 or something and enjoy the evolution of the genre. But if you did, then you know what I'm talking about.
Starflight: I have laminated maps from both Starflight and Starflight 2 hanging on my walls in here. I think that says about all that needs to be said.
