Is this in the iTunes Folder or in the actual iTunes app? If it's the app, there's a Show Duplicates feature built in that can be helpful in finding double ups. If you're talking about the music library folder, then changing the location of the library in the Advanced pane of iTunes Preferences and then pressing Consolidate Library in the Advanced menu will copy you files to a new location, leaving the redundant files (files that were not in iTunes, but still in the folder) behind.