Gtkpod could be better, I agree, but have you tried using
Amarok? I found it good, better than Gtkpod and
way better than iTunes itself. Much faster, more intuitive..and what's best, it works. Though I have to mention, the first time you use your iPod with it, you'll have to do some configuring -- in a correct order
it took me a moment to figure out how to do it, but after I succeeded (one evening without any specific help besides Google, took about a minute after I found the way) it rocked. Afterwards iTunes went crazy and didn't work with the iPod anymore, claiming it was broken, but Amarok deal with it perfectly (iTunes created a lockfile that it refused to remove, every time I tried using the pod, and only Amarok asked me if I wish to remove it).
So, before going crazy with iTunes I suggest you try out Amarok. The first time might (well, it
will) be frustrating, annoying and even desperate, but there's a clear way to configure the iPod and after you've done it your worries are gone. No 3rd party programs needed. And if you add a special transcode script to your Amarok (can be downloaded from the net), you'll be able to transcode© on-the-fly multiple music formats to your iPod, more than iTunes can handle.
If you need advice on configuring Amarok+iPod, I might be able to help. I don't have Amarok at the moment installed, but I think I can remember the buttons and menus which you'll have to go through in order to save the settings correctly..
