Best story in a game.Ever.

Eye of the Beholder, Baldur's Gate, Baldur's Gate 2, Icewind Dale, Icewind Dale 2, Neverwinter Nights and Neverwinter Nights 2 are all very close to the D&D systems of the time, storylines included. They are even officially supported by Wizards of the Coast if I remember correctly.
Also, yes I did read the manuals of the Warcraft games, it has been awhile since I read them and not much has stuck in my mind, so I would regard them as not being particularly good stories if they are so easily forgotten.

 

I would beg to differ, the story is of Arthas betrayal is more compelling than anything in Mass Effect so far. That said, it's still not the best story ever told in this format.
Planescape: Torment is the best "character's role-playing" experience I've ever encountered in a video game format.

A lot of people might hate me saying this, but some of the best stories in the video game format come from pre-2001 games. Deus Ex, Planescape:Torment, Grim: Fandango, Myst, System Shock 2, Half-Life, Starcraft (yes, it is good), Fallout (the ending oh my god), Xenogears (oh the complexity) just to name a few.

The best of the modern games has to go to Bioshock in my opinion. Still, it is pale in comparison to its spiritual predecessor that is System Shock 2 and Deus Ex.
Heavy Rain is not good. Maybe because I couldn't stand the uncanny valleys.

 

I never even mentioned Mass Effect...

Haven't played Heavy Rain, but pretty much agree with the rest.

 

The World Ends With You. Total Mind-blowing story... But who knows..

 

Stop spamming and you'd win, guranteed.

I just finished Hotel Dusk, and yea...*.* I loved the story. It's really good. Now...time to find that 2nd hotel dusk...