I'd say Persona 3: FES. To be fair, though, I haven't played Persona 4 yet.
Seriously, though, anything in the Shin Megami Tensei series is excellent. It baffles me how the gaming populace doesn't latch onto it.
People whine about how JRPGs do nothing but stagnate, while every SMT game (with a few exceptions) is innovative and tries plenty of new things. And, that's not even mentioning their fantastic stories that are just are rife with incredibly-placed symbolism...
...I should stop. I could go on for pages.