Chrono Trigger, because it is perfect.
Gameplay: Perfect
Graphics: Perfect for the time, amazing art direction
Music: Perfect
Story: Perfect
Replay: Perfect
After that, it's probably Final Fantasy Tactics, God Hand, Shadow of the Colossus, Secret of Mana, Hitman: Blood Money, LoZ: Link to the Past, Dragon Ball: AA, Link's Awakening and Genji in some order.
Gameplay: Perfect
Graphics: Perfect for the time, amazing art direction
Music: Perfect
Story: Perfect
Replay: Perfect
After that, it's probably Final Fantasy Tactics, God Hand, Shadow of the Colossus, Secret of Mana, Hitman: Blood Money, LoZ: Link to the Past, Dragon Ball: AA, Link's Awakening and Genji in some order.