Im not much into the FPS genre anymore, but when i did play there were some good times.
1st on my list is Soldier of Fortune 2. A "realistic" FPS that turned into a campy hilarious gorefest. I spent many hours on this one.
2nd the Quake series 1-4. Q4 kinda sucked, but it had its moments. I enjoyed the hell out of Quake 3 Arena, and its mods like Urban terror, and True Combat.
Unreal Tournament 99, and 2004: Another fun game because its campy. I havn't played 07 since i lost interest in FPS.
Return To Castle Wolfenstien: "Ze enemy ist VEEKEND!" Classic.. nuff said

Doom 3: What i thought was going to be just "Doom with enhanced graphics" turned out to be something totally different, and quite enjoyable. How many times did you get scared when a monster popped out of nowhere?
Of course lets not forget Classic Doom