If you have not already, I would recomend that you go ahead and update your iTunes as there are notacible improvements in both stability of Apps, and an amazing boost to the backup speed. I have 49 third-party apps as of now (not jailbroken...yet-waiting for Installer 4) and can get a backup of my iPhone in about 5 minutes. It used to take much longer.
When I first upgraded to the 2.0, my backup literally took over 3 hours with about the same amount of apps, and untl now, I have just been clicking the little "x" button when iTunes says "Backing Up" Just now it took me about 5 minutes to add about 15 songs and backup and sync!
