I'm yet another new Empeg user. The recent price drop means that I can finally afford the MP3 player I really wanted (previously had a Neo 35...), and I'm well impressed.
In order to transfer my existing MP3 files ("only" 3gb), I ended up writing a Perl wrapper for emptool (somewhat inspired by empsync). The tool uses the ID3 tags to automatically file the MP3s into suitable playlists on the Empeg. The tool includes a Perl module which provides a simple API to emptool, making it easy to write upload scripts for the Empeg. I've put the code at
http://www.ex-parrot.com/~pdw/empeg/
The only problem I have is that the upload tends to crash when trying to reboot the empeg after syncing a large number of files - have other people seen this with emptool?