- Chrono Cross
- Einhander
- Monster Rancher 2

gogogo
In addition to a lot of games already named, I really enjoyed SaGa Frontier. It had a level of freedom that's rarely seen in console RPGs.

Legend of Mana, too, although I never came close to finishing it.
In response to GITS-Motoko
If you save her you get korcha I think-cha. x:
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