You didn't find a solution to this did you?
I have the same problem and I'm running out of disc space (as an example I have 40 versions of Angry Birds, from 1.0.0.ipa to 2.0.0 1.ipa).
I've searched high and low on the web for a solution and most say iTunes should sort this out itself, but it obviously doesn't always... I haven't found a safe way to resolve it myself as yet (though I'm beginning to think I might have to uninstall and reinstall iTunes and see if that works....
(I'm using iTunes 10.5.1.42 on a PC running Windows 7)
I didn't, and gave up a long time ago. Although I'd love to find a solution and find it frustrating, it doesn't cause any noticable problems. iTunes and my iOS devices sync just fine. I just can't delete the old apps, nor does iTunes have any real way of helping me identify which exact file it is syncing with each device.
Tried the Genius Bar at the Palo Alto store, and they said it's not worth worrying about and they have no solutions for me anyway other than to delete the apps portion of the library, redownload my apps one by one, and then wipe clean the ios devices before resynching it all.
It's a nuissance, profoundly inefficient, and a huge waste of hard drive space, but I'm afraid I just don't have any solutions.
Thanks for your reply. I am hoping the new iTunes refresh or redesign rumored to be announced next week at WWDC will cure some of these weak links in the current design.
I have a question about the 2nd paragraph above. Based on the Genius Bar solution... deleting all apps from the iTunes on Mac hierarchy (just the apps section) then sync'ing from the iOS device to re -download them all back to the Mac... I follow that so far (and understand that any old apps no longer on the store should be safely moved outside the space first prior to deleting) but not sure why they then said to wipe the ios devices clean. What does that accomplish? You are already in sync at that point. I don't see a need to wipe.
I did the following on a PC running Vista but should be the same in Windows 7. In XP the iTunes folder will be under "documents and settings/yourname/...."
I made sure my recycle bin was empty and shut down iTunes.
I then went through the "Users/myname/Music/iTunes/Mobile Applications" folder and deleted all the but the latest version of each application.
I then created a temporary folder in the Mobile Applications folder and moved all the apps into that folder.
Next I restored all the deleted versions from the recycle bin.
Then I created another folder under "My Documents" folder and called it "Superceded apps" and moved all the files I just restored into it. (With 400 apps, this added up to just over 8-gig of files)
I then moved all the app files that were in my temporary folder back to the "Users/myname/Music/iTunes/Mobile Applications" folder.
Started up iTunes and performed a Sync.
So far, I've seen no ill effects. All my user generated data is intact.
I will be burning all the prior versions now sitting in the "superceded apps" folder onto DVDs so if anything "bad" happens, I can restore the old versions of any App that might miss them.
Hope this helps.