Linux on your iPod! Yes, and that link isn't the only one! People are determined to completely reverse engineer the iPod. Kids don't try this. Ever. Or grown-ups.
Actually, iTunes on Windows is a good bet if you can learn to encode using LAME, with the APS preset using other software. Then bring the files into iTunes. You might want to stay away from the 128 AAC format which Apple sells to innocent people--it is noticably inferior in sound quality when compared to a properly encoded music file. People fork out .99 because their ears have not yet learned to hear compression problems. Give 'em a year.
I tried both ephpod and anapod, but went back to iTunes strictly for management of the iPod unit. I do not use iTunes for ripping, burning, or music playback. This approach offloads iTunes's responsibilities, perhaps making it feel less cumbersome. The iPod plays back VBR MP3's that use the LAME encoder. Selecting the right tools for the various jobs has worked well for me. Good luck.