I have been using mine without problems, but a friend did lose all his data when he managed to freeze his system doing something bizarre.
Just plug in your pod, and Ubuntu will do the rest.
Only XMMS, installed along with the XMMS-MP4 plugin, seems to provide an easy way for you to play such files.
As for the protected AAC files you might have bought from the i Tunes store—well, forget about playing those back on Linux.
The filesystem format that is in place on your i Pod depends on which system you originally used it on.
If you first used it on a Mac, it will be in Apple's HFS file format.