Okay IMO the SNES era was a sort of golden era for turn based RPGs, considering the 16 bit capabilities it always felt like more development and thought went into the combat system and story (unlike nowadays)
Most of my favs RPGs come from the SNES library, but I would have to say my favorite is Final Fantasy 3 (6)
See to me this is the best FF period! The characters all felt unique to me with personalities that range from lovable dancing Moogles to mad men who who wish to dominate all planes of existance. The combat system worked very well, with abilities that were unique to each character it made it possible to develop several strats as well as add a dimension to the battle system that made each character different, also the esper system worked very, very well. The Espers would add stats when you leveled and taught you its magics which were gained on a multiplyer according to the spell. Not too many people realise this but you can also summon them =D.
I also loved the characters, Terra was just cool how the mystery played out for her, and you really felt for Cytan when his family was slain (wont spoil it for anyone who hasnt played it) as a kid it made me appriciate character development and drama pertaining the lives of the characters, all in all I would be a different person had I not played this as a twelve year old lol.
Thank you for reading and I hope to hear what your favorite SNES RPG is, =D