The only app worth using is pkgbackup and it costs money. Anything free (if there even is anything) is going to crap up your iPhone if you ever have to use it.
Pkgbackup makes a contact that contains data to tell what JB apps you have Once you sync contacts (or backup) the contacts of your computer will have this contact. If you ever have to restore, just sync or restore from backup, rejailbreak, install pkgbackup, and then have it reinstall all your JB apps or just the ones you choose.