James Farmer at WPMU.org wrote a very interesting Penguin-related article, which doesn’t make the update look too great, despite its apparently honorable intentions.

The update hit WPMU.org, sending it from 8,580 visits from Google on one day pre-Penguin to 1,527 a week later. Farmer shares an Analytics graph illustrating the steep drop:

Farmer maintains that WPMU.org engages in no keyword stuffing, link schemes, and has no quality issues (presumably Panda wasn’t an issue).

According to Farmer, the Sydney Morning Herald spoke with Matt Cutts about the issue (which may or may not appear in an article), and he provided them with three problem links pointing to WPMU.org: a site pirating their software, and two links from one spam blog (splog) using an old version of one of their WordPress themes with a link in the footer. According to Farmer, Cutts “said that we should consider the fact that we were possibly damaged by the removal of credit from links such as these.”

That raises a significant question: why were pirate sites and splogs getting so much credence to begin with? And why did they make such an impact that this site with a reasonably sized, loyal audience appears to be a legitimate, quality site, with many social followers?

Farmer wonders the same thing. He writes, “We’re a massively established news source that’s been running since March 2008, picking up over 10,400+ Facebook likes, 15,600+ Twitter followers and – to cap it all 2,537 +1s and 4,276 FeedBurner subscribers – as measured by Google!”

“How could a bunch of incredibly low quality, spammy, rubbish (I mean a .info site… please!) footer links have made that much of a difference to a site of our size, content and reputation, unless Google has been absolutely, utterly inept for the last 4 years (and I doubt that that’s the case),” he adds.

Farmer concludes that the site was punished for distributing WordPress themes. That is, specifically, for creating the themes that people wanted to use, and being punished because spammers also used them and linked to the site. He suggests to others who may have this issue that they remove or add nofollow to any attribution link they put in anything they release.

Hat tip to SEOmoz CEO Rand Fishkin for tweeting the article. Fishkin, by the way, has acknowledged that Penguin hasn’t been Google’s greatest work. He recently told WebProNews, “It’s done a nice job of waking up a lot of folks who never thought Google would take this type of aggressive, anti-manipulative action, but I think the execution’s actually somewhat less high quality than what Google usually rolls out (lots of search results that look very strange or clearly got worse, and plenty of sites that probably shouldn’t have been hit).”

The whole thing speaks volumes about what many have been saying about Penguin’s effects on negative SEO practices – the kind that Fishkin has challenged the web with. For Fishkin, however, everything seems to be going well so far.

Google is usually quick to admit that “no algorithm is perfect,” and I’m guessing they know as much about Penguin. It will be interesting to see if sites that shouldn’t have been hit are recovered in reasonably timely fashion, although at this point, it’s hardly timely anymore.