There are several ways of doing so, let’s discuss all ways that work effectively.
Method 1: Manually, APT backup.
Ubuntu/Apt users will find this handy
Step 1. Run the following command on iPhone Terminal:
dpkg --get-selections > /cydia-backup
Step 2. FTP/SFTP this file to your computer where you want to keep a backup
Step 4. SFTP the file back on the new jailbroken iPhone and run:
dpkg --set-selections < cydia-backup; dselectapt-get dselect-upgradereboot
That’s all. You should see all the packages back in Cydia.
Method 2. Automatic
Use a readymade app that does exactly that. Best apps are: AptBackup (free), PkgBackup ($2), AppBackup(free, backup App Store apps) to exactly that automatically.
AptBackup [from BigBoss repo] will make a list of your installed apps and put it in a location under the iTunes backup. So, when you sync on iTunes, the file is stored with the backup. So when you restore you phone, you just reinstall AptBackup and it will reinstall all apps back on to the phone.
You can also set it up for phone and use it as a template for setting up others with one click.
Although it will NOT, back up the actual app or its settings. Backup your springboard file placement. It’s not On demand restore. It’s only for restoring after a fresh iTunes installation.