I've only replayed:
Homeworld (because I wanted to play Homeworld 2, but I didn't get a chance until long after HW came out, so I replayed HW

)
Doom 1 and 2
Knights of the Old Republic
Republic Commando
GTA3 and San Andreas (mmm jetpack)
Civ 3 (several times)
Civ 4 (for Beyond the Sword, but essentially the game is the same)
Warhammer 40k Dawn of War + Winter Assault (2 or 3 times, mm)
Starcraft
I've replayed Alpha Centauri probably 10 or 11 times, that game is always refreshing. Sadly, there has yet to be a game that matches it
I tried replaying Rome Total War and Medieval Total War II, but I couldn't get back into it. The endgame in those is HORRIBLE. It's cool when you're still a small, fledgling faction trying to expand. The game becomes nothing more than a test of patience once you have a real empire going. Of course, maybe that's because I play beyond the victory condition and just try to rule the world... man, it's hard
Fallout 1 and 2
Geeze, there are a lot more in that list than I would have initially guessed