So a couple of weeks ago I took Billy's advice and went through all of the domains that were spammy links. We hadn't asked any of these places to link to us but there were almost fifty of them. I put together a spreadsheet of them all and the action we attempted to take to get the links to us removed and then sent all the information through GWT for a reconsideration request. On Friday, after having this manual penalty since February, we received the following note. I still think we may be under a Penguin penalty of some kind but I'll have to wait and see what happens to our rank after this.
Thanks for the suggestion, Billy!
Dear site owner or webmaster of http://www.aquinasandmore.com/,
We received a request from a site owner to reconsider http://www.aquinasandmore.com/ for compliance with Google's Webmaster Guidelines.
Previously the webspam team had taken manual action on your site because we believed it violated ourquality guidelines. After reviewing your reconsideration request, we have revoked this manual action. It may take some time before our indexing and ranking systems are updated to reflect the new status of your site.
Of course, there may be other issues with your site that could affect its ranking without a manual action by the webspam team. 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 your site continues to have trouble in our search results, please see this article for help with diagnosing the issue.
Thank you for helping us to maintain the quality of our search results.
Sincerely,
Google Search Quality Team