I use gtkpod, am happy enough that I have not bothered to try any others. I got my iPod (used), with about 2gigs of music and ebooks on it. I thought, probably easiest thing to do is install a Windows partition and install iTunes. First time connected to iTunes it was set by default to sync the iTunes database on my machine. Needless to say, I lost all that was on it. Second try with windows, iPod locked up.
Set up on Linux, installed gtkpod, and did not lose anything. All changes I make don't happen till I tell it to sync. It has never locked up on me under Linux, gtkpod interface is easy for me to understand, I still feel confused by my experience with iTunes, and have no intention to try it again. So I can vouch for gtkpod, great app. Maybe others can tell of experiences with alternate Linux iPod appz.