This is a really hard choice seeing that most of my favorite games are from the SNES. Such as: Chrono Trigger, Final Fantasy V (haven't finished VI yet so I cant include it), A Link to The Past, Super Mario World, Donkey Kong Country, Super Metroid, and Super Castlevania IV.
But If I had too choose a title it would be Chrono Trigger for its amazingly deep and interesting gameplay and story. I do have to say though that A Link to the Past would be second but only by a small amount