I have an iPod Touch, and one thing I've noticed is that even if I sync my apps to iTunes, iTunes never lets me drag my apps back onto my iPod Touch if I need to. I bought a new iPod Touch today too (updated to a 3rd-gen from 1st-gen), and I still can't drag my apps to the iPod Touch from iTunes. I've had to manually go into the App Store and download each of my apps individually. Why might iTunes not let me drag my apps to my iPod Touch?
I don't know if it makes a difference, but I have iTunes set up to sync manually rather than automatically (because I don't really want to sync ALL my mysic to my iPod).
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