I've been using Fruityloops for a good while now, and while it is pricey it comes with everything you need to make pretty much any kind of music, the rest is just gathering samples/soundfonts/synths/etc (Although It's fun to mess around with Slayer 2...)
Reguards to releasing the soundtrack as both Wav/mp3 and (MIDI I guess would make sense? If people were just after the specific notes). If memory served the guy that did the music for Kameo put all the midis on his site, and then had the mp3 version, after he'd sent the sheet music generated from the Midis to the orchestra, the end result. Was pretty cool stuff...
But I also agree and disagree with Battlerager, it's fun working out the notes for yourself, easier so if you're used to playing by ear, but some remixes I've heard deliberately have a wrong note or two and it just bugs me :p
Personally I wouldn't mind doing a few mixes from ear of the main theme, working it into a more sinister piece and also a fast-tempo boss encounter (I like doing those, personally

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