The Java-based Atmal bootloader software is JAvrProg, written by LadyAda. Once set up, it's very slick. Unfortunately, Java doesn't know how to work with serial ports out of the box, so you'll need to set it up first…
This isn't the easiest process in the world to do, but if you are careful, you can make it go
(WorkOnMe: need to finish off these instructions)
Many years later, I decided to upgrade to the Sokos OS. Thank god for this page, which seems to be the only place to find the required windows java libraries.
When I was setting it up, I had to make sure the files were in (jre)\lib\ext and then everything worked.
Assuming you've finally got Java IO working with your serial ports, you can finally run the bootloader.
java -jar JAvrProg.jar
If you're lucky enough to have firmware 1.03 installed already (Runs 2 and up), you can use c0ntr0l as a bootloader instead of JAvrProg. (FixMe is this still buggy and dangerous?)