Nope, nothing from Cydia or your jailbroken apps are backed up. The only things that ARE backed up from a jailbreak is anything you've done to modify the battery icon in the upper right corner, and anything you might have changed the "iPod" text to (for example, my touch that I restored to legit firmware and then restored from backup was exactly the same as a brand new touch, except for the fact that tapping the battery would bring up a percentage meter and the other corner said "iVan" instead of "iPod" - apart from that no other remnants of the jailbreak will remain).