The easiest way I've discovered is to do a two-fold backup: I use iTunes to backup the App Store apps and all their data, then I use the Cydia app PKGBackup to save all the jail break stuff.
Then, it's a simple matter of restoring the iOS, re-jailbreaking and then using the two backups to put the iPad back the way it was. Have a look at this link for further details on PKGBackup: http://www.ipadforums.net/showthread.php?t=60220
Again, this is how I do it and, so far (knock on wood), it's worked great and all my apps and data are as before.