I recently jail broke my 4S. Since the apps and themes that I purchased via Cydia are associated with my account, I've not worried about backing them up.
I use iFunBox. I've copied, modified, and restored files but not apps.
It's not necessary, but it's convenient to back them up with one of those 3rd party applications so that you can just restore everything you had installed all at once. I would only recommend doing it if you are restoring to the same firmware you made the backup from though. Lots of people ran into problems trying to restore their Cydia backups when they upgraded from 4.x to 5.x.