So I got the idea that it might be possible, since the iPod harddisk is much smaller than my "real" harddisk, to copy all of its contents on the PC harddisk, arrange the files as desired, and then move everything back onto the external harddisk, in the correct layout.
I don't believe this is that efficient as you will always need to copy all data from a slow HDD and then back even slower.
But if you want to test it. You could use a disk imaging tool that supports .VHD files and make a image of the iPod hdd then mount it as a local disk (builtin in Win7, Vista and XP needs extra software). Then defrag with MyDefrag, and when finished write the image back to the iPod hdd.
That's a good idea, I think I will try it.
I also expected that it would be a lot of work to implement. If I had sufficient programming experience I would try it myself, but I guess I couldn't manage to do it.
I still think it would be faster though, as the way MyDefrag works now also reads all the files and copies them back again, but multiple times, each file twice or more often in my case. But it would really only make a difference during the first run, so I guess it's really not worth it. I can wait
I thank you for considering it, though.