As iPhone users know, iTunes’ backup facility is sketchy at best; It can corrupt backups, it can be ridiculously slow, and on a personal note; I don’t like the idea of “trace files” creeping into a newly restored device.
So I’ve decided to outline a “workflow” I personally use whenever I’m up for a restore session. Everything here assumes a jailbroken device of course.
How it was before
On a 2.x device, the way you could get your AppStore apps’ settings restored was by using iTunes’ backup images – buggy as it is. There’s also the issue of bugs during normal usage; there have been cases of legitimate apps randomly crashing – and the only “cure” was to erase the app and reinstall it. This would’ve been fine, only they forgot to mention that when you erase/uninstall an app, that’s exactly what you’ve done – along with all its data.