Why won't apps on my iPhone sync anymore?

My system was getting really screwey, so I decided to reinstall OS X from the ground up (starting with Snow leopard, upgrading my way up to Mountain Lion). In doing so, I knew I'd have to re-sync my iPhone and iPad with iTunes. The iPad had no problem, it's syncing again just fine, but my iPhone didn't make the transition so smoothly. It syncs everything else, movies, music, contacts, but not apps. I've tried doing a backup of my iPhone, then doing a 'restore from iPhone,' hoping that would get it working right again, but no dice. What am I supposed to do to make apps synce again?? Strange that my iPad idn't have a problem at all, it syncs everything, including apps, just fine. And I *REALLY* don't want to have to reinstall things in a way such that I'd have to re-organize all my undreds of apps back into folders, I've done that dozens of times since I bought my first iPhone, and it's not fun.

Any advice?