A lot of contenders here. I'm gonna have to agree with all the people posting Planescape: Torment and Xenogears, since both of these games have incredible stories. Xenogears has the one flaw compared to Torment, however - it's too long for its own good at first, then cut. Hence, we have loads of padding on disc one, and then the second disc, where we get to the juicy bits, is pretty minimalist if, though I have to say it has some interesting presentation. Torment, on the other hand, is short and concise. A bit too short, even. So yeah

I'm also gonna add Persona 3 and 4 here, since those were amazing (Innocent Sin was great too, butI haven't played Eternal Punishment, so I don't really know the whole story), as well as FF Tactics Advance. It and Tactics have probably the best stories in the entire franchise. To hell with the X hype

Still, I don't think any RPG may rival my favorite video game story of all time. That title has to go to Silent Hill 2.