I'm assuming you mean games where you directly pilot a ship?
X3:R (as people have already said) is a great 3D game, especially with a joystick.
Star Control II/The Ur Quan Masters (UQM being a remake of the ancient SCII, for modern computers) is a great choice if you like top-down spacey shooting with a keyboard.
Yes, I was looking around to see if this would be mentioned, and so far, it's the only other time it was mentioned. I'm in agreement to this game, it's one of the greatest sci-fi experiences to ever grace the computer screen.
Get it. Be a *happy camper*.
The X-Wing series was pretty awesome too. Tie Fighter has, by far, the best story; but if you want to orchestrate a crap-ton of battles (skirmishes and melees), have tons of ships to include in battle (up to 12 ships per team, or 8, or 6, or 4, or 2, or 1; and with a bit of modding, pilot Star Destroyers and such, and have starship vs. starship matches as a starship), and even fly through the Death Star II tunnel, play X-Wing Alliance, and go to XWA Upgrade for graphics more fitting to your graphics card and today's standards. It's still in development, and these guys are awesome.
Darksaber's site (link within) should have a packaged file that can install all the updates as they are/been released for you; sometimes a surprise addition comes along ripe for downloading. He's done a fair share of the upgrade modeling. You gotta compare what the game originally had with the upgraded versions. Be amazed.
Son of a....you just made me reinstall that when I get home, and break out my venerable Saitek and hope it still works.