Top 3 is very hard to choose, cannot filter..............too many good games.........overall......
1. ICO and Shadow of the Colossus
2. The Legend of Zelda: Wind Waker, A Link To The Past and Ocarina of Time.
3. Mirror's Edge
That's 6 in my top 3....and Portal should be in there as well.......and Resident Evil 1....yeah........Im not very good at this.
As for racing games/sims.....
1. RACE 07 (for the online racing)
2. netKar Pro (for the physics and FFB)
3. GPL (for the awesomeness)
honourable mentions.....
Tourist Trophy
Gran Turismo 1, 2, 3 + 4
GT Legends
Shooters......
1. Battlefield Bad Company 2 (still the pinacle of modern shooters)
2. COD 4 (first ever online multiplayer for me)
3. STALKER: SOC.