Deus Ex (the original): 20+ times. I lost count but I always have at least 1 playthrough a year on top of the 10+ times I played it through when I first got it. Every now and then I'll still find something I didn't notice before or rediscover something long forgotten. Amazing game.
Final Fantasy VII: Probably around 10 times now
Dragon Age Origins: 6 times
Mass Effect 1 & 2: 5 times each
Half-Life 2: 6 times
Uncharted 1 & 2: 4 times each
I play most WRPGs, Metal Gear Solids, Tomb Raiders and FPS' at least twice.