You might want to check out jempeg by mschrag and dzimmerman. It is a java clone of Emplode. It is not perfect, but it will allow you to drag and drool your whole mp3 directory over and figure out what files are new and only upload the new ones. It has some ID3 tag issues, but asside from that it works pretty well. It is also open source so you can tweak it to meet your needs.

-Mike

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EmpMenuX - ext3 filesystem - Empeg iTunes integration