I'll also exclude action RPGs and PC titles.
The Suikoden series is damn fine, I like Final Fantasy 6, KOTOR and Xenogears.
Eternal/Skies of Arcadia is also a phenomenal title, Earthbound is cool and I drool whenever I play an early Breath of Fire title or any Dragon Quest/Warrior game. My tops fighting engine would go to Grandia II, as well.
My favourite ever?
That's really, really tough. I know, I know you said RPG and not RPGs but it's tough!
Chrono Trigger, probably. Haven't played it since elementary school, but I remember working that game to the bone with a friend of mine. Second, in my opinion, would be Panzer Dragoon Saga.