Define "best story"?
If it's the best story, if it could be implemented as a book's plot, it's Xenogears/Planescape: Torment (and 99% of whoever thinks differently didn't play these games, FACT).
MGS games have a well polished plot, but otherwise simple ones, while MGS4 doesn't have a good story for itself, but as a conclusion to a saga.
Final Fantasy X? Think back about it, realize that it... just doesn't.
KotOR? Think back about it, realize that you can sum the story in three lines.
Chrono Trigger? Again, a very simple, but highly polished story.
Final Fantasy VII has to many boring characters, though the story is quite good.
Bet with Dr.A.Peter.Nintendo that Super Mario Galaxy 2 won't sell 15 million copies up to six months after it's release, the winner will get Avatar control for a week and signature control for a month.
