1. Deus Ex Human Revolution
2. Bioshock
3. Crysis 2
4. Call of Duty Black Ops
5. Resistance 3

Deus Ex and it's not really close for me, unless you disqualify it because they're heavily RPG's.

Bioshock, though, I didn't find it particularly strong in gameplay. It had good gameplay, and had some neat powers. But it wasn't near as polished as half-life 2, or even call of duty (shooting mechanics wise). Nor the role playing elements of deus ex. But still, it's story and atmosphere more than made up for it.

Half life 2, I find a bit dated mechanically (except that it uses health packs instead auto regen hooray!). its still great no doubt. But it used to be one of my top 10 games, and it's fallen quite a bit after subsequent playthroughs (which all my top games go through).

Halo (Except Halo: Wars, because it's a RTS as you probably know)
Half Life 2 (+ episodes)
Crysis (2 is my favorite)

No only story wise. Still an excellent game on its own.

Oh yeah Crysis series would also be a good choice for a singleplayer FPS.
The Darkness series too, but that one is kinda short

I didn't know you could play Crysis games! I thought their sole purpose was to be mentionned in best graphics thread!

To everyone mentioning Metroid Prime, I have played all Prime games (and love them), although they're from the first person perspective and you do a lot of shooting, I think of them as Metroid games first which is why I don't include personally include them with other FPS games.

Half-Life!

I personally like the Metroid Prime series a lot. Funny thing is that most Nintendo fans claim that it isn't a FPS.

For the sake of all that doesn't suck though, don't ever try Metroid: Other M. I love Mr Khan, but his opinions on the game are warped.

Bioshock wins. No contest.

The first 2 Halo's had sweet campaigns.

Resistance 2 has a crappy campaign.

Where is Half Life?