The backup process on the Apple iPhone and iPod Touch appear to take a very long period of time, sometimes several hours or more. I assume transferring all of the data over USB 2.0 just takes a very long time. I also think if you store a large amount of email messages on your phone that it significantly increases the backup time. When I am in a hurry and can't wait for the backup process, I usually click to cancel the backup so that the synchronization process is triggered. When I get a chance, I will be looking for some other work-arounds here.