2 options:
You can still make a backup while jb'ed. Plug in to iTunes, right click on the iPad in the left column, choose Backup. Once done, click Restore in the main info window. The iPad will restore to factory settings, and you can then restore to the backup you just made. It only restores your data and settings, not the jailbreak.
Other option: just plug in and Restore. It will be like a new iPad, so you'll have to set everything up again from scratch.