How to copy folder settings from iPhone to iTunes 3G

iTunes corrupted its settings on my Mac yesterday. I managed to get it to see my music and my apps again, so on the desktop everything is now working OK.
However, it seems to have lost all my apps settings for my iPhone. When I tell it to sync my apps it shows me that its going to copy all the apps across onto my iPhone again. This wouldnt bother me, except that its going to wipe out most of the folders that I painstakingly copied all my apps into.
Does anyone know of a way to import the folders (or the folder settings) into iTunes from an iPhone (sort of a Senuti for Apps)? Googling etc has only revealed that others have had the same problem, but Ive not yet found a solution (or the right keywords for Google...)
Steve
Intel iMac 24" Mac OS X (10.5.8) iPhone 3G (4.0)