Half-life 2, Halo 3, COD4: Modern Warfare, Bioshock, and soon to be Halo: Reach.

Honestly? I liked Prey the best for campaign all around. The tweaks were just enough to keep me quite interested, despite its shortcomings. I very much liked the flipped gravity and the out-of-body gimmicks. It's one of the few FPS campaigns I played through multiple times gladly. Portal is obviously brilliant, though I don't think it's really an FPS so much as a puzzle game with an FPS camera. I personally wouldn't count HL2 either as "this gen". It was released in 2004, and I'd say this gen started in fall '05.

Honorable mention for Bioshock, Halo 3 and COD 4/6 for excelling in certain areas, though each had its flaws. (Bioshock - ending and "hallway syndrome" too often, H3 - story, COD 4 - monster closets and cheap deaths, COD 6 - preposterous, ridiculous, ludicrous story).

Didn't play KZ2 campaign, so can't judge that. Resistance campaigns were just ok for me, though #2 had some cool moments. Battlefield campaigns suck, IMO.

Half Life 2(I wouldn't count it though as it was released before xbox 360 and it was released on the original xbox)
Then Bioshock, or Crysis Actually, the story was bad but the gameplay was fun as hell.

Resistance 2 for sure..imo

I'm sorry but I simply found Half-Life 2's narrative stronger.

Half Life 2 then Portal. Any other SP campaign I've played (and I like FPS SP campaigns and have played pretty much most of them) this gen has been week with the exception of Bioshock which was okay but fell apart at the end and lost focus partway through. I'm just getting around to Bioshock 2 finally but it's too early to tell on that one.

Resistance 1 actually had a pretty fun SP campaign but 2 I felt lost the plot a bit too much although it was still a pretty decent SP campaign.

Not finishing Half-Life 2 is my secret shame.  I own it, so I'm just waiting for it to come to Steam for Mac to finish it.

You must finish it. It's an amazing game.

Killzone 2 or Bioshock for me.
But CoD4, MW2, Resistance 1+2 and Bioshock 2 were great, too.

(btw.: The worst was FarCry 2 IMO)

Bioshock and Resistance 2 are still my favorites.

Side note: If you're going to type out "in your opinion", why put "iyo" also?