I like for iTunes to keep my music library organized. There's an option in the iTunes preferences for that. There is also an option to automatically copy any song that is dragged into the library to the directory where you store your files.
I have one directory on a server that is shared throughout my house and that folder is the default folder for iTunes to store music on. For example, the address of the music folder is //server/music/all the folders where all the folders is what iTunes keeps organized. Problems arise when users add a song to their library that is already present, or they accidently buy a song we already have, or they've reinstalled itunes and accidently copy songs over and over as itunes rebuilds the library.
Fortunately their are a couple of iTunes conventions that I am taking advantage of to try and automate the process of removing duplicate songs from the music folder.
The Goal of iTunes Duplicate Song Manager:
To create an automated process to automatically remove duplicated song files from the iTunes library folder and safely move them to a backup folder. This program will be written in Java to facilitate both Windows and Macs.
This project is also being used to help fulfill requirements in my Software Engineering masters program I am taking at the University of West Florida. The program caters to those who already work full time and allows students to finish their masters within 1 year. I have a similar project going on for another requirement at another blog as well.