Jeffrey Ross said:
The greatest FPS of all is and forever shall be the FPS sections of Banjo-Tooie.
SO TRUE. I loved those!
In all seriousness though
My favorite FPS is split into many different categories, since you can't really group it all together.
Favorite Multiplayer: Halo 3, I spent a lot of time in that game, I just love the battles, not long like health based shooters like quake and UT, but longer than "I see you first" battles of games like call of duty. BR is my hero.
Favorite casual: Doom 3, after I beat it once, I just play nightmare from time to time, I just love bunny hoping around the levels and killing enemies while they don't stand a chance, makes me feel awesome.
Favorite Single Player: Half life series, half life 1 and the expansions were early for my time, so I didn't really like the narrative and such since it wasn't really there due to limitations, but HL2 and its expansions were just mind blowing, I'd never seen a physics engine like havoc before, and the gravity gun was just way too awesome, everything about it was awesome, from catch with DOG to the mysterious encounters with the G-Man.
Favorite Coop: Borderlands, for easy reasons. It was just plain fun.
Favorite Game due to community: TF2 PC, the stuff that goes on in the game is just awesome, all the new weapons and hats were something that just made an awesome game cooler, some of it contributed by the amazing community, all of the memes, videos and jokes that have come from TF2 are just mind blowing. I don't think there will ever be a community so rich with awesome in a long time.