We recently told you about WPMU.org apparently getting hit by Google’s Penguin update. The site went from 8,580 visits (pretty standard for the site, having looked through the Analytics myself) to 1,527 a week later. It’s been hovering around similar numbers ever since, with a pretty clear dip right around Penguin time.

Do you think this site deserved to get hit by Penguin? Let us know in the comments.

We spoke with James Farmer, Founder and CEO of Incsub, which runs the site. Farmer maintains that WPMU.org engages in no keyword stuffing, link schemes, and has no quality issues. In fact, the site has actually done well throughout Google’s series of Panda updates.

Farmer tells WebProNews, “We did great after Panda, it was like that update recognized we were decent folk… you can’t win them all huh?”

“Apart from not being able to guess what Google was going to do in April, 3 years ago, we haven’t done anything wrong,” he says.

Last week, Farmer received some second-hand info from Google’s Matt Cutts, who reportedly spoke with the Sydney Morning Herald about WPMU.org. According to Farmer, Cutts provided three problem links pointing to the site. These included a site pirating their software and two links from one spam blog using an old version of one of their WordPress themes with a link in the footer. Farmer reported that Cutts “said that we should consider the fact that we were possibly damaged by the removal of credit from links such as these.”

It’s pretty interesting that if such links were the problem that it could have such a tremendous impact. It’s no wonder there have been so many discussions about negative SEO (competitors attacking each other with these kinds of tactics) since Penguin launched.

The site has over 10,400+ Facebook likes, 15,600+ Twitter followers, 2,537 +1s and 4,276 FeedBurner subscribers, according to Farmer. Apparently not enough to outweigh some questionable links from third parties.

“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),” Farmer wrote in his article on the matter.

When asked how many links he has out there just from footers for WordPress themes, he tells WebProNews, “Given that we stopped adding links years ago, actually not that many at all.”

“However, the challenge is that given that we provided themes to a lot of multisite installs, which have since become overrun with splogs, there’s an enormous amount of links from not that many actual root domains,” he adds. “I’d guesstimate 1-2K, 99% of clearly low quality sites.”

We asked if he’s heard from other WordPress theme creators, having similar issues.

“Actually no, although that doesn’t surprise me that much,” he says. “Not many folk are as open as us, and in this field they probably have good reason to be. WordPress terms are very, very competitive so I wouldn’t be surprised if 9/10 competitors had something to hide!”

Like many webmasters, Farmer just doesn’t know what to expect from Google, in terms of whether or not Google will consider the site to be one of the innocent casualties of Penguin.

“I have no idea, I would love it if they did. I guess the thing I’m begging for is some sort of qualitative mechanism (NOT the manual webspam web, faster approach) that allows quality operators, like us, to survive and carry on providing Google users exactly the kind of helpful content they need!”

Google does have a form users can submit to, if they think they’ve been wrongfully hit by the Penguin update.

Google’s Matt Cutts recently told Danny Sullivan that Google considers the Penguin update a success, despite the large number of complaints from those commenting on blogs and in forums. Of course, the Penguin update, much like the Panda update, should be periodically coming back around, giving sites a chance to make fixes and recover. That also means however, sites will also have more chances to get hit.

We asked Farmer if he thinks Penguin has helped or hurt search results in general, outside of his site’s issues.

“Especially in the WP field they have gone wild,” he emphasizes. “For example our flagship site WPMU DEV – if you go to search for that now a competitor writing something ridiculous about us and copyright appears above our massively popular Facebook page. It even looks like our YouTube channel has been demoted. Crazy stuff.”

We’ve certainly seen some other questionable search results following the update, and others have complained aplenty.

Do you think the search results have improved since Penguin? Should WPMU have been hit by Penguin? Share your thoughts.