I think that the best FPS games are Call of Duty: Black Ops and Call of Duty 4.
There were others that I would call my favorite, but most of them were destroyed by people who like to cheat and use game hacks.
Counter-Strike 1.6 is the best FPS of all time...however, that's only if you're counting league play - all public servers are filled with cheating, shit-talking, prepubescent children.
If you're not talking league play, then I'm going to have to say MW2.