purplekitty - 9:56 pm on Apr 29, 2013 (gmt 0)
I was hit about a year ago by Penguin for two of my sites as well. It really surprised me since I've tried to always follow the guidelines set forth - build for your website for users, not engines - and I didn't engage in link building schemes.
Anyway, I sent a reinclusion request to Google for one of my two sites a few months after that because I figured I must have been hit by a penalty of some sort, and was told about a week later that there was no penalty. That left me having no idea, really. In Bing and Yahoo, I still am on the first page of the serps for popular keywords phrases, but in Google, I lost them all. It made no sense to me.
I finally posted in the webmaster community asking for help where I was promptly called a spam link farm and basically mocked there by a bunch of users. So helpful. Not.
A couple of people took time to actually offer some insight into what Google might see when looking at my sites. Apparently, these two sites that I've been building for 8+ years that are different topics, but have some cross-over, are looking like link farms to Penguin. Well, I didn't cross-link to game Google. I cross-linked as appropriate for my users who would get value out of both sites.
So I figured out a way to add nofollow to my links since the sites stand on their own and now I sit. Waiting. For a Penguin update. And hoping that the nofollow will fix whatever Google sees wrong with my websites.
Interestingly, the site sitting in 1st place for the top keywords for these two sites are link directories maintained by the same person, both of which link to my websites' pages (ie. BlueWidgetDirectory links to many sites about BlueWidgets, including mine. RedWidgetDirectory links to many sites about RedWidgets, including mine). I've also seen a number of Pinterest boards getting some pretty great rankings on page 1 & 2 for these popular keywords. All of which I think is weird if Google's goal is to offer the most relevant results.