I was doing a sync on my iPhone tonight, first one on iTunes for ages and it was a pain in the derriere. It kept hanging and I had to force quit several times, it was hanging when trying to copy Myst so I ended up having to delete it off my iPhone. Once that was done things started to move again.
Another annoyance, and one I just cannot fathom is its insistence on copying every single app downloaded from the AppStore back on to whatever device is attached. My son's iPod Touch also syncs with iTunes on my MacBook Pro and I have downloaded some games for him onto his Touch. This device uses my Apple account but has a different name yet iTunes insists on transferring every one of those apps onto my iPhone which is annoying. Why does it do that, perhaps there is a seperate setting to stop this happening. It doesn't do it with music playlists so why with software?
I ended up spending about 40 minutes trying to sort everything out and by the time I was finished I was so cheesed off I couldn't be bothered to do the v3 iPhone software update. In fairness to iTunes, this is the first bit of hassle I can recall in using it.