This is exactly my current situation...
As a result of the SEOMOZ Duplicate content report I set about resolving these issues...
In the first instance I configured URL parameters via Google Webmaster Tools. It instantly occurred to me that whilst this fixes these potential duplicate content in Google this configuration does not affect other search engines and the work is unlikely to be reflected in future SEOMOZ crawls of the site.
I'm interested in creating a over arching method of removing the potential duplication caused via URL parameters required to paginate, sort and filter content. The majority of these URL parameters are standardized across web applications. But is it actually required?
In my case each Magento store uses the canonical tag correctly and has an updated robots.txt to restrict the crawling of areas of the site that should be excluded... In a sense this is the over arching method of removing potential duplicate content. So why is SEOMOZ reporting duplicate content?
I suppose the big question is... Is SEOMOZ crawling the site correctly, do these results reflect robots.txt and canonical tags?