Well I can't say I have a favorite one since I am a general rpg fan, I will mention notable ones. The ones that someone worth's playing.

Chrono Trigger, of course, end of thread!
Final Fantasy VI, of course end of thread!
>>4 Zelda, it is an rpg althought a very unique one.
Sword of mana!!
FF IV
FF V
Live A Life have you played that? it's nice.

I will post again when I remember anything else.