Interesting. I would speculate that the home page link penalty has to do with the old standard where a link in the footer to the home page was used to reinforce the main keyword theme for the site, such as "Power Tools" or "Sporting Goods".
I used to do that myself on sites years ago, but I also began to think it was detrimental and stopped doing it a few years ago. I agree with one of the posters in WMW that this penalty has probably been in place for a while.
I just checked rank positions today after setting up about 7 or 8 links over the past week. The main keyword theme for the site dropped one rank position, but related combinations have all gained from 1 to 20 positions. That could be in line with the theory that the main keyword phrase for the site should be avoided in internal links to the home page. In this case, the main keyword theme is in the home page HTML title tag.
The home pages for a lot of the sites that got hit by Penguin have never recovered for their primary search phrase, but inner pages have recovered for long tail keywords.
This all appears to make sense to me and may have something to do with Penguin's overoptimization of backlinks penalty--only this variation applies to internal links.
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