mslina2002 - 12:43 pm on Sep 19, 2012 (gmt 0)
I suspect it's the footer links in the templates.
netmeg is right.
Google does not like those backlinks. It may have been fine before but this has changed. What was OK 10 years ago, may not always going to be OK now.
Here is another example, take a look at WPMU.org and how they got penguinized due to their footer links.
post: #4464063 by rlange
The SEOmoz Blog has a post titled "How WPMU.org Recovered From The Penguin Update". The specific situation may not apply to everyone hit by Penguin, but it might offer some clues.
The gist of the solution is that they removed something like 500,000 backlinks with anchor text that may have looked suspicious (footer links in WordPress themes they offered). Those backlinks were on a domain offering community blogs using their themes. The domain was also under their control, though, so they had it easy.
If you google the analysis you will find a detailed analysis of how they recovered from Penguin by removing those footer links.