Update 9/14/2008:
Backup speed was addressed in iPhone software version 2.1. Launch iTunes, dock your iPhone, and click “Check for Update”.
And now back to the original article:
I was surprised to see my brand-new iPhone 3G taking more than 15 minutes to synchronize with iTunes. It would get “stuck” in “Backing up iPhone…”
It looks like there are two reasons why the backup process takes longer — iTunes backing up newly-installed applications, and MobileMe/iSync database cruftiness. Expect sync’ing to take a while if you’ve installed new applications. If you haven’t installed new applications, you should try resetting the iSync database.
It’s pretty simple:

- Close iTunes.
- Start iSync
- Click iSync > Preferences.
- Click “Reset Sync History…
The next time you sync with iTunes, the “Backing up” step should be dramatically shorter.
Another interesting solution involves Vacuuming your syncdb. If you’ve got MacPorts installed, it’s easy:
sudo port install sqlite3 sqlite3 \ ~/Library/Application\ Support/SyncServices/Local/data.syncdb\ vacuum