PkgBackup has been getting better and better ever since the first release. I can honestly say this was the first time that I was able to backup and restore and not have to move a single icon when it restored. Springboard files put everything right where they were before the restore (did restore as new and reloaded all apps fresh from iTunes subsequently). If you follow the right sequence, it will all be there. The only issue I had was the new App store data library restore feature didn't work (i.e. for Angry Birds), but because I had the data libraries backed up via DropBox I was able to SSH the data files in and save my previous scores.
Just to be clear, here was my process with PkgBackup v4.3.5 (beginning after the iPhone has been upgraded to new firmware version):
Install PkgBackup & restore:
- Cydia Sources
- Jailbreak Applications
- Preferences files
- Springboard files
- Apple defaults apps.
Then reboot and:
- Restore App Store Apps (either from a fresh install or a restore from iTunes
Launch PKGBackup to:
- Restore App Store Data Libraries
- Springboard files (if iOS overwrote my SB icon layout)