1)
Quakeworld: Perfect blend of speed, skill, teamplay and excitement. Must be pretty damn good for me to still be playing it over 10 years after I started

2)
Far Cry: Probably the best single player FPS I've played. Fantastic graphics and (relatively) open-ended approach to the many varied levels.
3)
Deus Ex: Great storyline and characterisation, it successfully managed to blend FPS with RPG while also featuring one of the best designed levels I've ever played (Hong Kong)
Ask me another day and I might choose differently however. KOTOR, COD and NFS5 (Porsche) all run it very close for 2nd and 3rd places.