Super Metroid rocked. The Final Fantasy games have always had good to great music. The Zelda games are good, especially a Link To The Past on the SNES. There's a ton more I can't think of off the top of my head.
But my favorite of all time is...
The Secret of Mana (SNES) Square released this sleeper in 93. I played the heck out of it. Some in the music in that game was incredible, other parts were just ok. But overall it has the best music in my book.