Here are some of my favourites, or at least ones I like:
Dark Chronicle (Or Dark Cloud 2, whatever)
Drakan: The Ancients' Gates
Dragon Quest: Journey of the Cursed King
Eternal Ring (it's not for everone, but I really enjoyed it.)
EverGrace (Again, not for everyone. I'm one of the few people who liked it.)
Grandia II
Phantom Brave (Mix between strategy and RPG.)
Phantasy Star Universe
Rogue Galaxy
Shadow Hearts
Devil Summoner (...Not for everyone. I still count it as one of my favourite games, for the PS2 at least. I would also say the 2nd one, but I've never played it due to some douchebag who decided not to release it en Europe.)
Persona 4