Man, this would be immensely long. I'll just name a few off the top of my head.
Fire Emblem
Golden Sun
Final Fantasy IV-VI (PS1, GBA, and DS for IV, yes, I own multiple versions, have beaten none) Edit: And SNES for VI
Killer 7
Paper Mario: The Thousand Year Door
Metroid Prime 2
Persona 3: FES (in progress)
Lost Odyssey (in progress)
Wild Arms 1 & 3