I am the product manager of the MyBackup product line at RerWare, LLC.
To let you guys know, we have just released "MyBackup Root", which is a FREE download from the Android Market. It is for root phones only, and it will BATCH BACKUP AND RESTORE all applications, including the Data\Settings and Market Links! You are also allowed to schedule backups. All FREE.
We want to support the Root community, so we have made this a Free application, please help us spread the word!
Try it out, we would also love feedback MOD EDIT: REMOVED EMAIL