Backing up Cydia apps has always been a pain! Different implementations exist with little or no success. I recently lost all my Cydia Apps since I thought I backed them up just fine (using AptBackup which can be installed from Cydia). How to save hours trying to get back all the apps installed in Cydia? And here goes the step by step guide to achieve it :

Test environment : I have used AptBackup while restoring iPhone 3G from 2.2 to 2.2.1 firmware on a Mac. I used iTunes 8.0.2.

And here goes the step by step guide to achieve it :
1) Install AptBackup and OpenSSH from Cydia
2) Launch AptBackup on Cydia and hit the ‘Backup’ button

3) Make sure SSH is on and backup the 3 filesaptbackup.cydiasources.tgz,
aptbackup_dpkg-packages.txt and aptbackup_openssh.tgz found at ~/var/mobile/Library/Preferences (this is a precautionary step, just in case AptBackup fails)

4) Connect iPhone to iTunes and let it fully backup (you may click the sync button iTunes as well)
5) Restore to the firmware of your choice (in this case a custom firmware 2.2.1 with 2.28 baseband)
6) Jailbreak using QuickPwn if you didn’t use custom firmware in step 5 and install AptBackup and nothing else for now
7) Now connect to iTunes and restore data from the latest backup (iTunes should automatically prompt you)
8) Now launch AptBackup and hit the restore button, it should take a while depending on the number of applications you backed up from Cydia. It should then automatically install them for you while you were waiting!

9) Just in case AptBackup didn’t do what it was supposed to, install openSSH and restore the 3 files to ~/var/mobile/Library/Preferences you backed up in step 3 and then launch AptBackup and hit restore!

If you follow these steps closely, you should easy succeed backing up and restoring Cydia apps, an increasingly important routine with frequent firmware updates from Apple!