Out of the ones I've played:

1. Star Ocean: Till The End of Time (no, I'm not kidding)
2. Final Fantasy X
3. Persona 3: FES
4. Final Fantasy X-2
5. Persona 4

Star Ocean 3 was arguably the first forward-thinking, post-modern jRPG thanks to the ridiculous twist towards the end, so for that alone it gets infinite praise from myself.