Thes apps… they aren’t huge. I don’t know exactly what is being backed up when iTunes tells me it is “Backing up ‘iPhone'”, but it is taking an elephant’s age. If it’s not the apps, is it the sql lite database? Whatever it is, if you install a few apps on your phone, have something else you can be doing while it syncs up.
Update: the iphone is synced and now none of my downloaded apps work. Awesome!