iTunes does not screw up your music files, or take them over.
when you install iTunes it asks you if you want iTunes to ORGANIZE your music files, if you say yes, then it will just move the files in to organized folders inside an iTunes folder.

it does not change the format of the music unless you ask it to.
where you need to be careful it importing music from cd's in to iTunes.
it will import them as AAC files (which other apps support, but some do not).
you can change this in the settings to import in a specific format of your choice, along with quality options.

buying music from iTunes , the files come down as AAC, and without copyright. meaning you can buy a song from iTunes, and it will be playable on any device you own, including your droid!

iCloud also has a new option, when you buy a new song on iTunes on your PC, it will automatically dowload it to the rest of your iDevices (optionally). this is great if you don't want to connect your iOS device to your computer so often.

download it on iTouch, and it will automatically be on your iPad and PC (iTunes).