Xenogears/Xenosaga... complain about too many cut scenes all you want, but at least they made sure the story was told right.
Vagrant Story
Saga Frontier
Every final fantasy EXCEPT for VII... every other final fantasy was great, but VII was Die Hard meets Captain Planet.
Grandia
Star Ocean
.//hack
Chrono Trigger, Cross, and (if they're still making it) Break
Lunar Blue
Arc the Lad
Legend of Dragoon
Dragon Warrior
Vampire: The Masquerade (both redemption and bloodlines)
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Yes, I played too many video games growing up... but believe it or not, I did learn what creates a working story better than I did dissecting books or movies, because my characters had to live with how I did things. Chrono Cross in particular spelled elements like that out to me. Even if I outgrow them someday, I still owe them that.