I'd say that the most overall polished FPS I've played (so far) was Half Life 2.
As its style/themes appeal to me it also remains my favorite.
Honourable mentions though to the founding fathers (Doom, Doom2) and to recent highs like COD4.
I actually prefer Deus Ex / System Shock 2 overall but I don't consider them 'pure' FPS and more of a FPA (First Person Action) game that happen to have some shooting but plot/puzzles and the narrative are much stronger and important.
Try to be reasonable... its easier than you think...