I have been using gtkPod and also amarok, but sometimes I just missed that iTunes interface to sync with my iPhone 3GS (16GB).
Well, with using the virtual box ( you will need to get the Sun version and not the OSE (open source edition) because the Sun edition has the USB parts)
Then I booted up the virtualbox with a Windows OS, and installed the iTunes I was able to sort out my iPhone in the apple way!!.
It is still kinder annoying that apple are not making iTunes for Linux, but with this setup at least I am able to still use the iTunes interface with my phone and sync correctly.