I know it may seem that I'm not talking about mp3tag as such but I found this very useful program for deleting empty directories. Seeing as mp3tag is music tagging software and everyone likes to keep there music organised. So this is just an extension to that by clearing out any empty directories that you may have lying around. I found that itunes even when you have the keep music organised [x] leaves some empty files lying around in your music root directory.
Here's the link http://www.jonasjohn.de/red.htm