Bioshock for sure... this is the best I have seen this generation.

The worst is MGS4...

Special (negative) mentions to Killzone 2 and Halo 3.... can FPS have some sort of stories please ??

did you think about ... maybe ... (climax music)... Bioshock 

seriously you mentioned Bioshock then complain about no stories in FPSs come on man =P

ff7
bioshock
uncharted
oblivion

Hey Bioshock is no real FPS like KZ2 and HALO 3.

It has the same roots has the System Shock series... more like an hybrid adventure/shoot.

Fire Emblem!!

I could compile an overly long list with games that I think have great plots and/or storytelling, but I'll keep it to two franchises:

Ico / Shadow of the Colossus
Half-Life 1 and 2 (Episodes, obviously, included)

Omg I forgot the Half-life series...

Mass Effect had a fantastic story
Uncharted had a very well told story, though it may be a little clichéd

Call of Duty 4 could also be considered to have a decent story, but again, I think that is just very well told

Metroid prime 2... It's so good because you have to figure most of the story out yourself by scanning dead bodies. You can listen(ok, read) the stories of a lot of luminoth(aliens) before they died because of the dreadful ing. It's very very sad and beatiful to read it and there's just so much to read.

The first Half-life and the first Fallout.