Gotta go with Rise of the Traids, myself.  In my opinion, this game revolutionized the head-to-head aspect of FPS, introducing a variety of game types beyond the standard deathmatch.  It was also one of the first to have a truly 3d environment.  Compare it with Doom 2, the other major FPS at the time.

Close behind this is Doom 1+2 (not 3), Half Life 1+2, Goldeneye, and Halo.