Probably Xenogears.
FF6, FF7, and Chrono Trigger tie for second place.
I'm playing FF7 on PSP now. I'm so pissed that a bunch of Square PSX RPGs got released on PSP in Japan but not in the US.
I also really liked Saga Frontier II. I seem to be alone in this.
What's the deal with CRPGs anyway? Is it just me or did they forget how to make good ones with compelling stories after the PSX? FF8 lacked a soul and FF9 was pathetic. I stopped playing new FFs after that. Actually, I tried XII but it quickly bored me.
On the other hand, Disgaea was fantastic. But it's not quite an RPG.
Did good CRPGs die in the 90s?