"PXTONE is my third generation sound editor. Originally it was intended to develop background music for games in a 80's style. It turns out to be a convenient resource for those who are looking to integrate their own sound waves." -Pixel
Scared off by the Japanese on the site? Don't be. Gryzor87 (of Hydorah OST fame) has recently created what appears to be a very robust manual.
"This manual is dedicated to all videogame lovers and musicians. It has 96 pages fully illustrated, 18 songs, 57 examples and 92 voices to choose. There are also detailed explanations for songwriting, tips & tricks and recommended stuff as well. The Great Pixel, author of Pxtone, has written the foreword. If you think it’s worth it, I accept a donation." -Gryzor87
It's all free. Check it out.