I have two sites, one was hit by the first launch of Penguin, the other was unaffected until the refresh. Now it has been blasted.
What I did was to try an experiment, and although it was only one site and therefore can't be real evidence, it may be something to think about.
I am active on a number of SEO forums, and before the last Penguin refresh I changed my signature link to point to my second site. I didn't do anything else to the site, I didn't get any other links and I didn't add anything or take anything away.
But from having 30 keywords that were in the top 50 Google results (many on page 1/2), after the refresh I had nothing at all in the top 50.
The ranking of my main site has not changed appreciably, but although Google has picked up the new links to the second site, it is still showing most of them as still being active for the main site.
The anchor text was varied, and the links were not all to the home page. Although as I said at the start this is just one site, it does lead me to believe that irrelevant signature links can actually be harmful.