Final Fantasy 6, closely followed by Chrono Trigger and Secret of Mana.
FF6 had the greatest villain in any FF game, Kefka wasn't only pure evil, he was batshit insane, he had no idea what he was doing, and he completely destroyed the world so he could rule over the chaos. He had no dream of a new better world, he didn't even care that the world was his, he just wanted the world to match the inside of his head. It was great.
Chrono Trigger was great as well. I had started to forget about the game after a few years when Chrono Cross came out and tied itself in to CT. Needles to say as soon as I finished CC I was plugging my SNES into the TV and running through CT one more time.
Secret of Mana was a great action/RPG with a great score and an interesting story, considering it was one of the first for the SNES it hold up very well to this day, I recently played through it on my Wii and remember everything from when I forst played through it. Great game.







