I don't think I saw
DOOM mentioned. The Classic Doom3 mod proved the concept (if you haven't tried it and still have you Doom3 discs lying around, DO IT, NOW!), now it needs a real, full release with all three episodes.
Oh, and turn the demons pink again mmkay?
I am
kinda curious what
Star Control II would be like with modern graphics and such, but on the other hand I think it might lose a lot of character in the transition. Maybe just bring it up to par with the 3DO version.
In the same vein but much older:
Starflight. Don't even have to bring it up to modern times, just re-make it on par with Star Control II's 3DO version. That'd be awesome.
Duke Nukem 3D. It'd be way better than DNF. Sure there's sourceports and the Hi-Rez pack, but it could be so much better..
And finally,
Herzog Zwei. This very early RTT might seem primitive to some, but I guarantee you it still has plenty of fans. Grab a Genesis emu and a rom of it and find out why.
Previous suggestions I agree with:
X-Wing/TIE Fighter series
Wing Commander series
Deus Ex
Syndicate
Cannon Fodder
Blood/Blood 2
System Shock 1/2