Half-Life 1 and 2 were the most boring pieces of crap (although I haven't given HL2 a big play yet... so I can't really judge that one all that much)
Deus Ex is hardly a purebred FPS... and it was WAAAY too complicated for my liking. I like my gaming simple and fun. That's why Dooom III was so unreal. Back to basics... good atmosphere, good level design, good monsters, good weapons... awesome game.
Quake 2 had it all. It was the first FPS to really bring a sense of immersion to the genre. Instead of just going through level after level shooting everything you saw... you were a MARINE, you had things to DO... and in between that you shot everything you saw. It was fun, it awesome, and everything about the game rocks. It still is (in my eyes) the best multiplayer FPS there has been. Back before CS came along and completely killed multiplayer gaming Quake 2 was where it was at. Closest thing gaming got to an art-form.