Solved
SOLVED...
Sorry for digging up this old post, but it applies to my problem. I've been unable to get apps purchased via my iPhone to sync up with iTunes. I've tried to Transfer Purchases and syncing applications under the applications tab for my device. I've also tried this on two different PCs, both having the same result. I see the applications installed on my phone (3Gs/3.1.2) but no apps are listed in the list on the left and no amount of syncing, attempting to delete apps, etc. has helped.
Edit: OK, so I just now bought an app through iTunes app store and it shows up in my applications list, but the ones purchased via the phone still do not show up in the list.
Edit 2: When trying to move the newly purchased app to my iPhone from iTunes it warned me about not being on an authorized computer. Authorized and all apps transferred over.