great storyline? FF6. I'd still love to see them make a movie out of it and put it in theatres with redone musical tracks.
I also loved Sou Kai Gi by Yukes (published by squaresoft). It was about a group of special young talents preventing these ancient people from destroying japan by summoning these gates (which released all kinds of demons out). which was nice, because each of the characters was affected by these events in thier own way. The voice acting was excellent. The only really bad thing was the graphics and controls, but I overlooked that for story. I believe it was based on a book as well.
Crono Trigger, FFVII, and I'm particuraly biased to FFVIII seeing it was my first RPG, but I loved the cast and characters in that game 馃檪
Zone of the Enders: The Second Runner also has a storyline that is unparalleled in the world of robots and such, I highly recommend 馃槃