"Clean install" means different things to different people.
You might intend to erase the entire hard drive, then reinstall OS, apps, data, and all. Official instructions here:
http://support.apple.com/kb/PH14243
You might intend to reinstall just the OS. Official instructions here:
http://support.apple.com/kb/PH13871
IN EITHER CASE, make a full backup of your HD beforehand.
There's little point to being selective about what you backup, since chances are, if you are selective, you'll end up erasing something that you forgot to backup.
The time to be selective is when you're putting stuff back onto the HD.
Like the song says, "Don't it always seem to go that you don't know what you've got 'til it's gone?"
If you don't already maintain a Time Machine backup, get yourself an external hard disk and do it. You can then restore anything and everything you may need to restore.
http://support.apple.com/kb/VI29
Just so you know, if you're just reinstalling the OS... app settings (like iTunes) are not deleted.
And if you do want to be "selective" - backup the entire iTunes Library - that covers music, settings, and all.
http://support.apple.com/kb/ht1751