BC2 on 41? I'd say that could be a little higher on that list.
CS on 39? Same goes for this, deserves a higher spot imo
L4D2 on 34? L4D1 on 33? Great games, sure, but I'd say L4D2 is better than L4D1.
Halo 2 on 31? Halo 2 wasn't all that great imo, and that's coming from a Halo fanboy
Halo Reach on 24? I really enjoyed Reach myself, but as far as I know most people don't like it thát much.
Deus Ex on 24? should be higher imo. That game was like a (human) revolution back then! (See what I did there?)
TF2 on 23? Sure, fine.
Crysis on 17? Meh, it wasn't thát great, but ah well.
Halo 3 on 15? I agree with that, sure : )
MW2 on 14? No, it's a good game, but not as good as Black Ops, for that matter.
Bioshock 2 on 13? Bioshock 1 was _way_ better than 2 imo.
HL2 on 12? I was hoping this would at least be in the top 3.
Portal on 10? I wouldn't call Portal an FPS, as it completely lacks the "S", a great game, but again, I wouldn't call it an fps.
Bioshock on 6? Well, disregard my previous statement about BS2, they put up BS1 on a higher spot : )
Halo: CE on 5? I fully agree with this.
Half-Life on 2? I was really expecting this to be number one, close enough though.
So yeah, I agree with some, I disagree with others, but that's what lists are for.