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There are million of various theories out there about how to find out if your site is penalized by Google. I thought I’d recap what Google officially says, and by officially I mean on their domain and bearing their brand. Their help system is a bit scattered so I may have missed some.
1. Verify that your site ranks for your domain name (reference)
Do a Google search for www.[yourdomain].com. If your site doesn’t appear in the results, or if it ranks poorly in the results, this is a sign that your site may be penalized for violations of the webmaster guidelines.
Brian White of Google notes that inside Google the nomenclature with the brackets used above indicates what is actually typed in the search box. So when they say to search for www.[yourdomain].com, they actually mean that you would search for yourdomain and not include the www, com, or the surrounding dots.
2. Message Center (reference 1, reference 2)
If we find certain problems with your site - for example, malware - we’ll let you know via the Message Center
we launched Message Center in our webmaster console, which allows us to send messages to verified site owners.
3. PageRank of Zero (reference 1, reference 2)
Google believes the site violates our Webmaster Quality Guidelines.
4. Removed from the index (reference 1 , reference 2 , there are more but you get the point)
If a site has been penalized, it may no longer show up in results on Google.com or on any of Google’s partner sites.
and
if our review indicated that you engaged in deceptive practices and your site has been removed from our search results
5. Noted on your Summary Page (reference)
Your page has been blocked from our index because it does not meet the quality standards necessary to assign accurate PageRank. We cannot comment on the individual reasons your page was removed. However, certain actions such as cloaking, writing text in such a way that it can be seen by search engines but not by users, or setting up pages/links with the sole purpose of fooling search engines may result in permanent removal from our index.
Note: Emails from Google were stopped in August 2007 due to spoofers and scammers.