Today had some issues with gtkpod not starting up due to a dependency problem with a library.
I gave amarok a shot since it boasts iPod compatibility as a feature.
To cut a long story short amarok completely screwed up the itunes database and my iPod refused to play at all after loading some new files, so you might wanna stay clear of amarok to update an iPod nano (found a few posts on the net mentioning problems between amarok and the nano), for other models I cannot tell since I only own a nano.
I finally found a version of gtkpod I could install and was able to restore my database and can now access my music again.
Just fyi.

