1) Terranigma
2) Zelda A Link to the Past
3) Super Metroid
4) Zelda Ocarina of Time
5) Super Mario All Stars
Terranigma was an experience like no other. I didn't think it possible for Quintet/Enix to do better than Illusion of Gaia, yet the sequel surpassed even Zelda, mainly thanks to its incredible (and moving) story as well as charismatic characters. But of course these elements alone wouldn't have brought it anywhere if the game didn't also feature excellent gameplay, combining action and puzzles just perfectly.
Additionally, it still has my all time favorite soundtrack (counting both games and movies)
A little note on Mario All Stars: I would have voted for Mario3, but I only consider it better than Mario World when allowing you to save and restart from any visited world, so...
Pity I couldn't fit Metroid Prime in there, but I see it's getting enough votes anyway.
