From the October Google Webmaster Chat Q &A:

Anonymous: Sitemaps question - How do we know what pages in the sitemap are NOT indexed? The report shows us how many are in the submitted sitemap and how many are indexed, but not which ones are or are not indexed...

JohnMu: One way you can do that is to set up separate Sitemap files for the different parts of your website. Doing that you can find which areas of your site are not being crawled and indexed as much as you would like. Perhaps you'll also stumble upon areas that you don't want indexed completely?

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