Simsi - 8:16 am on Jun 23, 2012 (gmt 0)
I still think there's a strong correlation between an un-natural backlink profile and Penguin.
Question relating to adder's OP though. You mentioned site-wide links. Simplifying the question, if a site has 100 inbound links and 95 of those come from one site (say, a site-wide footer link) with the same anchor, could that disrupt the link profile?
On the one hand, it might explain a problem I am working on, on the other it seems a recipe for negative SEO.