If I was to go by the amount of time I spent playing it, and the fun I had, I'd say that it's a close one between Goldeneye and Perfect Dark on 64. Brings back happy memories of grades 7 - 12. My friend and I recently got our hands on a second hand 64 and got Perfect Dark and Goldeneye, as well as a tonne of other games, and finished them all again. 😄
At the moment though, my favorite FPS would have to be the two S.T.A.L.K.E.R. games.
Half life and Half life 2, plus the expansions are also a couple of timeless games IMO.
Man, I f*cking love computer games, really I do. 😄