There's so many great retro songs (both retro as in actual old game music and retro as in style)
Megaman 9, Galaxy Man. New, but yet still classic:
Megaman 3 opening. This one pretty much defines my childhood:
Some snes goodness, Darcula X, Bloodlines:
Not from a game, but could just as well be, while ironically being used in a game... ,
Same artist, another of my fav tracks he's done:
This one is from MMZ2. It's probably one of the best uses of music and images to build up for the final confrontation in a game, before or since (though the vid in the link is just the song and artwork) Maybe not that retro conisdering it's a somewhat recent title, but the limitations of the GBA makes it count if you ask me.
Overworld from Terranigma. One of the SNES's best games by far. If you haven't played it.. do it!
Some Castlevania 3
Beginning, from Metal Gear. The game might be a bit crap of a port but this song is awesome =)
And of course, Cave Story =D
(I love this one)
That's it for now. =P