The webmaster thought his site violated some guidelines but to his surprise, it did not violate a guidelines that was manually triggered. Google said there was "no manual action" taken against the site, but the site still may be suffering due to automated algorithms that feel the site is not worthy of ranking high.
Here is the Google response:
Dear site owner or webmaster of http://www.example.com/,
We received a request from a site owner to reconsider http://www.example.com/ for compliance with Google's Webmaster Guidelines. We reviewed your site and found no manual actions by the webspam team that might affect your site's ranking in Google. There's no need to file a reconsideration request for your site, because any ranking issues you may be experiencing are not related to a manual action taken by the webspam team. Of course, there may be other issues with your site that affect your site's ranking. Google's computers determine the order of our search results using a series of formulas known as algorithms. We make hundreds of changes to our search algorithms each year, and we employ more than 200 different signals when ranking pages. As our algorithms change and as the web (including your site) changes, some fluctuation in ranking can happen as we make updates to present the best results to our users. If you've experienced a change in ranking which you suspect may be more than a simple algorithm change, there are other things you may want to investigate as possible causes, such as a major change to your site's content, content management system, or server architecture. For example, a site may not rank well if your server stops serving pages to Googlebot, or if you've changed the URLs for a large portion of your site's pages. This article has a list of other potential reasons your site may not be doing well in search. If you're still unable to resolve your issue, please see our Webmaster Help Forum for support.
Sincerely, Google Search Quality Team
I've never seen one of these responses yet but I know Google has been sending them for the past few months.
The webmaster is now asking himself, what do I do now?
So he is currently working on technical issues and other basic SEO implementations to try to get his site ranking well in Google.
Forum discussion at WebmasterWorld.