Create and backup a list of all your Cydia installed packages:

(1) Login via SSH into your iPhone (check old posts to know how to do that)

(2) Create a list of all your via Cydia installed packages by using this command:
dpkg -l | grep ^ii | awk '{print $2}' > /private/var/mobile/Media/installed.txt

(3) Copy the file “installed.txt” to your computer using SFTP or e.g. DiskAid.

Thats it. Now you can safely resotre or upgrade you phone. Make sure, Cydia is installed by using QuckPwn or PwnageTool.

Re-install all packages:

(1) Make sure you install OpenSSH with Cydia. Open Cydia, search for the OpenSSH package and install it. Then install all Repositories you had installed before: Open Cydia, go to “Sections” and open up “Repositories” and choose all you used before. Otherwise Cydia will not find all packages to restore.

(2) Copy the file “installed.txt” back to your device using using SFTP or DiskAid.

(3) Login into your iPhone using root:

ssh -l root (IP-number of your iPhone)

(4) This was edited and updated, so only new packages will be installed. Enter:
dpkg -l | grep ^ii | awk '{print $2}' > /private/var/mobile/Media/installed-new.txt
then
diff /private/var/mobile/Media/installed-new.txt /private/var/mobile/Media/installed.txt | grep ^\> | awk '{print $2}' > /private/var/mobile/Media/installed-todo.txt
then
apt-get install `cat /private/var/mobile/Media/installed-todo.txt`

(5) You will not see all installed applications, because the iPhone did not re-spring. So the easiest solution would be a “reboot” –> reboot now!

That should be all