Finally, after years of asking for it, Google now let site owners know about manually applied penalties.This information is easily available now through the Google Webmaster Tools site at http://www.google.com/webmasters/tools under ‘Search Traffic->Manual Actions’.  Apparently 2% of sites have a manual action against them.

For background Google has two types of penalties, algorithmic penalties are in their ranking algorithm and are automatically applied and removed as necessary – this includes the Panda and Penguin updates along with a whole host of other penalties. Manual penalties are applied by someone in Google after they have reviewed your site, and can only be removed by someone at Google. In order for manual penalties to be removed you need to file a re-inclusion request, no such request is required for automatic penalties.