To answer Tedster's question, the only thing I did with the meta was the title, which unfortunately is an annoying global title applying to all pages. I got the webdevs to make it flexible and pull in the category titles and apply them. But this is the ONLY change on-site. We also re-balanced the anchor profile, changes existing keyword anchors to brands. Still no recovery yet. Again, our other information (but commercial) site has not been touched.
Diberry, I think that is an interesting question. Contrary to the theory, I was reading a post by Aaron Wall on his private forums where it was suggested that weighting may even be given to linking out to quality sites. If your links are carefully selected high quality sites, it would be a worry to understand you have been penguined because of it. Because Google thinks you're trying to be smart.
And herein lies the confusion, we both have observed a situation where Penguin appears to be working against its own concept. I'm not always a skeptic but I wonder if there is a degree of misdirection in Google's official line, getting us all focused on de-optimizing our sites so that Google doesn't have to work harder to find those that ARE good at SEO. Kind of like, handing us a loaded gun and saying we're the enemy.