I did it finally. I've been able to sync my iPod under Ubuntu. Now, I cheat a little bit and I use Windoze XP running in a virtual machine, but it works! This is the last hurdle for me to cross - managing my music under Ubuntu.
Using Virtual Box, I am able to run Windows XP on Linux, and inside that, I am able to run iTunes. I keep all my music on a removable USB drive, so I am able to access it by mapping the removable drive to my virtual Windows.
Virtual Box supports USB connections to the guest machine, but only with the non-open source version of the software. It is still free, though.
In order for the guest machine to recognize the device, you have to setup a USB filter. I'm not sure what you are filtering, but it makes it work.
Once you have it connected to your virtual windows, the sync takes a while to start, but it really works.
Now, all isn't well. There is a known bug that some applications have problems writing to mapped drives from the guest machine. ITunes is one of these (Microsoft One Note is another); trying this causes a blue screen of doom. But I was able to get around this.
I started iTunes on my guest with a new library, all on the virtual machine. I was able to purchase a song from the ITMS and save it in the virtual machine. I then closed and re-opened iTunes, with my real, mapped drive music library and added the newly purchased song to my library.
It is a little inefficient and takes up some more disk space, but it is much better than making a 40 GB virtual machine in order to store my music library inside. Now, with a little cheating, I can using iTunes Music Store and sync my iPod, all under Linux.