Damn, I was just about to start with a multiplayer game (Wolfenstein: Enemy Territory). Anyway, my list is probably something like this:
2. Quake II
3. Wolfenstein 3D
5. Call of Duty
6. Far Cry
7. Return to Castle Wolfenstein
8. Red Faction
10. Doom 3
And no, I don't consider Deus Ex a first-person shooter, it's more of an RPG to me. Also, while probably more like a simulator, I'd probably list Operation Flashpoint here had I played it more (I'm just beginning). And then there's tons of great games I haven't played.
And please note that first-person shooters aren't exactly my favorite genre (well, I do love Wolfenstein: Enemy Territory, probably so much that it would be in my top 10 of all games of all time, and it would be pretty high on that list).