one thing to watch out for is that iTunes Backup ALSO backs up some of the jailbreak data and directories.
I know this because with each new update (4.0, 4.1, 4.2), I did a full hard reinstall of the iOS. I think it was with the 4.1 install I did a restore from backup after the install. Then I jailbroke the iPad. When I went into the directory structure with SSH I found that much of the data from the previous jailbreak were still there, just with slightly renamed directory titles (the titles had a period with random characters following it).
This also happened on my iPhone. This is problematic since previous jailbreaks appear to eat up storage space on the device (example, old Winterboard theme folders and items, etc).
Once the 4.3.x jailbreak is released I plan to restore my iPhone as a clean slate, no restore from backup, jailbreak it and go in with SSH to make sure the OS install (even a full install) isn't just ignoring these jailbreak directories, then clear them all out.