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iTunes recognizes my iPod on my PC, but it doesn't show up in "My Computer". What's the name of the program that let's you transfer files (apps for example) to it?
Are you jailbroken? You'll need to be in order to transfer anything other than music / photos / bookmarks type stuff via iTunes.
If you are jailbroken, you can use WinSCP or other SSH apps to transfer stuff back and forth wirelessly, or something like iPhone Browser to do it when you're connected by cable to your PC ...