iTunes pisses me off. A lot. And heck even if I wanted it I couldnt use it (Win98 FTW). So what d'y'all use?
Can't use use WMP with iPods? I don't know because I have a Zune.
I use Xplay for my Windows machine, and Banshee on my Linux box. Xplay allows you to drag and drop files and automatically converts them for you. You can also copy songs to your computer.