"Galbadia Hotel" has a huge number of soundtracks, popular and rare stuff, but they're always down and some of their links don't work. Just Google Galbadia Hotel.
"Blue Laguna" doesn't have as much stuff, but they have a great collection of more modern RPG music and I've never had any problem with them. [Link removed by moderator - no links to illegal content]
More and more, people are using Youtube to upload and collect BGM into playlists. This is a great alternative to collecting MP3s which takes up memory and may be virused.
And of course, some fan sites post whole collections of music like Secret of Mana and Mega Man. I don't know of any specifics off the top of my head, mostly because they usually get shut down quickly, but they do exist.