I've had my ipod for a few weeks now. I've deleted iTunes and use MediaCenter for most things related to the ipod. I have purchased "Anapod" to help me manage the iPod, it integrates the iPod right into Windows Explorer.
http://www.redchairsoftware.com/anapod/I do notice that while tracks are being converted from APE to MP3 and uploaded to the iPod, that I can't "see" the tracks on the iPod (using Anapod) until the iPod is "ejected" In fact there have been a couple of times where MediaCenter has spent HOURS converting and uploading music and then I don't eject right or something and the iPod has none of the tracks.... I wonder if it would be better if MediaCenter did some kind of "commit" after doing some number of tracks to prevent a total loss of work in case of an error.
One really cool thing is how MediaCenter updates the playback stats on connect, even when the formats are different, it updates my APE files with changes made to the iPod MP3 files, pretty neat.
iTunes is so lame (for Windows anyway), I think I would have returned the iPod if that was all I had to manage it. How did I ever live without MediaCenter?