Yakuza 3. It had a slow start since it was mostly used for character development and setting up the plot, but after that, it turned into a fantastic experience. I laughed, cried, felt rage, and I stood in awe when it was over. Sega better localize Yakuza 4 fast!!

Folklore gets an honorable mention. I love those murder-mystery stories.

For me I would have to say the best story for any PS3 game... and perhaps any game I've played is Valkyria Chronicles.

1. Uncharted 1/2
2. Valkyria Chronicles
3. Yakuza 3
4. inFamous (loved the plot twist )

Metal Gear isn't really my type of game, so I can't comment on that but my favorite story on my PS3 has been Uncharted: Drakes Fortune.  In fact, I think Uncharted is my favorite "everything" on my PS3!  IMO it was that good.

Definitely Yakuza 3.  The story was just amazing.  You'd have to play it to understand it.

InFamous had the best ending but Heavy Rain had the best overall story.

Uncharted 2

My personal pick would be Bioshock. Followed by Infamous

MGS4 for me. Honourable mentions for Uncharted 2 and God of War3 (the ending was something)

Uncharted 2 for me has the most consistently and well told story even if it is basically an Indy level romp, so I'll put it first for the consistency and clear confidence of the developer.

Valkyria Chronicles was also well told in a consistent manner, so I'll put that second.

Heavy Rain is arguably a deeper and more involving narrative than either, and when it clicks its exceedingly good, but it had some hiccups here and there with narrative flow IMHO, and boy was Cage so clearly wrong to remove the scenes explaining Ethan's blackouts... so I'll put it third.