That can be tough.
For the most engrossing and complex story: I would go with Xenogears for the PS1.
You could list any Bioware game, but Mass Effect for its beauty and innovation, Baldur's Gate 2 for its lasting appeal, and Star Wars: Knights of the Old Republic for allowing everyone to really experience being a jedi. Oh, and all Bioware games have that great "Moral-meter" factor. Don't forget to check out Dragon Age: Origins coming out soon too, will be a hit.
Call me crazy, but in Final Fantasy terms, I go with FFVIII and FFX. Just loved the stories.
All time best though? Probably Xenogears. Just loved it.