It is a hard call. Several games in the FPS genre has given me a phenomenal gaming experience.
Doom had it going because of the emergence. Play it with stereo sound, and it was just scaring!

Dark forces had the whole starwars theme going.
Rise of the Triad (rott) was quite fun, but never "the greatest experience ever."
Duke Nuke'em 3d just a classic. Great one-liners, Schwarzenegger in a game

Shadow-Warrior, also by 3Drealms, even better. This time you have the Nuke.
Jedi Knight is also a great game. Really one of the first games that used a consistent story-line. Great in multi-player too.
Half-Life the first one with all the story taking place inside the game engine. Great idea.
And let us not forget GoldenEye64. First game with independent body parts. Shoot your enemy in the head and he dies.
The entire Quake series, as well as Unreal Tournament, enhancing on-line gaming.
Doom 3 and the expansion seems to be my favorite at the time. I just admire the way ID manages to get the effects across on the screen. Just amazing.