Aydin chronicles, I know is almost universally hated, partially I think because the game is more of a crpg, when most people wanted some kind Final fantasy clone.
I loved the big world and it's sense of wonder, adventure and exploration, the interactions with the characters and the fact that you needed to dig up yourself, most of the world lore.
Ogre Battle 64, great, but man o man the alignment system can fuck you up.
The Goemon games.