I love my iPod but... I have had two occasions when iTunes or my iPod ends up corrupting some files in the hidden
directory \iPod_Control\iTunes\ on my iPod. It seems this problem is wide spread over a number of iPod models. This forum entry sums up the problem and some solutions really well. The most annoying thing  about this problem for me is that it leaves my iPod in state of having music files on it but the index file is corrupted. The rest of the iPod is otherwise fine. This means my iPod thinks it has no music on it when it actually does. Because I sync my iPod from a couple of different locations and carry a good few data files on it as well, I find restoring my iPod to be a really annoying task because I have to copy all my files off it and then back onto the iPod post an iPod updater restore. Even with USB 2.0 this still takes a long time with a nearly full 60GB iPod.

To try and avoid this type of problem in the future I have implemented a simple "last known good" database backup script using a good old .bat file. This backs up the important iPod database files to a backup dir but excludes the Music dir so the actual mp3 files are not backed up as well.

So in practice I run the backup after I have finished syncing with iTunes but before ejecting the iPod safely. I have tested this working by manually corrupting some files in the \iPod_Control\iTunes\ and testing a restore and this seems to work.

Hopefully those familiar with batch files can follow whats going on here. Please note I offer no guarantees on the success of this method and please use this at your own risk. Also keep in mind that really important files should be backed up on multiple physical media and kept in different locations to be safe.

rmdir iPod_Control_Backup /s /q
xcopy iPod_Control iPod_Control_Backup\ /s /e /h /y /exclude:excludebackup.txt
pause

It would have been great if Apple could have thought about providing a better solution to this problem with what I will call "logical disk failures". I guess Apple are considering the possibility that there could actually be some real "physical disk failures" starting and it might be hard for software like iTunes to able to tell the difference between logical and physical failures?

Anyway, good luck with your iPods and don't forget to back up really important data.