I had the opportunity to speak with a penguin troubleshooting expert yesterday, and his message was very strong and very simple. He is a speaker at a lot of industry events.
1. Do not, repeat do not, build links to your home page. Only build links to interior pages. If the home page gets penalized, the whole site gets hammered. If an interior page gets hit, only that page gets penalized.
2. Penguin is all about anchor text. He recommends keeping your money keyword anchors under 10%. His analysis is that the value of keyword anchors is close to zero. Google is getting its topical signals from on page seo, and on-site links.
If you want a page to rank for multiple keywords, use them as internal anchors on your own site.
Every site that he cleaned had anchor text issues, and when the anchor text got fixed, the rankings came back. I can attest to this. We got hit on October 3. We control some client websites with footer links to our site. We got stupid and put exact match anchors on them. It threw off our anchor text %.
When we got penalized, it was only the pages that had the links pointed at them. Furthermore, once we changed the anchors to branded, and had the site crawled, our rankings came back.
Peguin 2.1 was not a big mystery. It targeted anchor text% at interior pages. The fact that specific pages got hit instead of the entire site is what threw people off.