Top 2 are easy, for 3rd place though I have like a million way tie.
1. S.T.A.L.K.E.R. Shadow of Chernobyl
2. Hitman: Blood Money
and...
3. Final Fantasy VII: Crisis Core, Portal, Oblivion, Fallout: New Vegas, Starcraft - Brood War, Diablo II (with LoD), Just Cause 2, Mario and Luigi Superstar Saga (I really miss this game now), Heroes of Might and Magic III, Persona 3, Minecraft, NBA Jam (for the Sega Genesis, now THAT was a good sports game), Perfect Dark, Mario Party 3, N+, Fire Emblem, Fire Emblem - The Sacred Stones, and the classic Doom games (1, 2, Final 1, and Final 2)