Doom is the ONE for me, I mean, using a source port like ZDoom along with utterly awesome modss like Alien Vendetta, Hell Revealed, Herian II, Void and all these great things, It just amazes me to see what can be squeezed out of the engine, and to this day, more and more gets made for it!

After Doom, I would say Unreal Tournament...you gotta love the HEAD SHOTs XD

After noticable mentions include Quake 3, Hexen, Strife, Duke Nukem 3-D and Exhumed

I like my old school simpler FPS games