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No - I am afraid that as far as I know if you are going to use iTunes then you cannot tell it not to backup the Stanza data. iTunes simply backs up the data for every installed application so that it can later restore the data if required. However once you have let it do the large initial backup of Stanza data later backups should only back up changes.
Having said that if you untick an application in the Devices app tab and then say no to the prompt about uninstalling the application I am not sure what happens. If you want you could experiement.
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