Really, in my opinion most of the popular fan games have great sound tracks.
The last comer, mystical power plant, riverbed soul saver
white name's spoiled past, book of star mythology, youkai kori kassen
marine benefit, shining shooting star, bullet and music (that's literally the name of the game)
Mrs. Estacion
Len'en's sound tracks are questionable, people tend to either love them or hate them, but personally I enjoy most them.
Mythical Mirror has a stellar sound track, but it's a bit of a shitty game.
Nansei, Heavenly Gathering of Clouds, and Treasure Castle Labyrinth are all pretty good, though they're just sound tracks and not actual games.
Those are just the obvious ones off the top of my head.