Super Mario World.
Even if my loyalties moved more to the disc based console, SMW still holds a special place in my heart. The music, the colors, the gameplay. The joy of stepping over a Secret Palace Switch and returning to a level to see stacks of blocks now filled was unparalleled. The pain that was beating most castles, particularly the sixth one. Timing had to be impeccable.
Playing a game with so many secrets to unfold and such a satisfying gameplay is what makes this game stick the most for me in the 1990s. I still stand that Nintendo hasn't done anything this good ever since.