I'm going to have to say ALttP. Second would be Super Mario All Stars or Super Mario World.
I haven't played too Many SNES games. I just wish my grandmother wouldn't have given the SNES away with all of the games. (it was a fairly decent collection.) Of course, she picked it up in a garage sale I believe and She gave it away when she decided to move thinking we wouldn't miss it with all of the modern games and systems we have.
I can't choose one. Final Fantasy VI, Super Mario RPG and Chrono Trigger are probably my top picks, but Zelda: ALttP and Final Fantasy IV are also very strong contenders.
As of now, I'm going to scream Super Mario RPG: Legend of the Seven Stars. That game was absolutely amazing and despite never having beaten it (farthest I got to was IIRC right before Smithy's stronghold...or maybe right after the Axem Rangers?), the time I DID have with it was just amazing. Never got to beat that superboss (Crystal Weapon??). Never beat the final boss though he looks crazy hard. Never got to grind for realz. I hope it gets a remake for Wii U or SOMETHING.
I've never played ALTTP but my favourites for the SNES are: Super Mario World (the first game I played), all the DKC games, Super Mario Kart and Mario All Stars.