Update 4-18-13: I was kindly contacted by one of the Disqus Developers who worked on the issue discussed below and fixed it. You are no-longer in danger for your rankings in Google (at least not in a direct way that I can see) from using Disqus. As a matter of fact, using Disqus now that the issue is solved can actually help you get some internal page rank flow and increase your visitors on-site time (something Google actually loves). They added a NoFollow tag to all external content which should make Disqus Discovery safe when it comes to SEO.
So I finally decided to give it a try and monetize my main website. I was getting fair amount of traffic and near instant rankings for whatever I wished to write about. So, I decided to implement a simple ads section facilitated by Disqus, the amazing commenting system that allows you to keep track of all the comments you make online. I wanted to use something unique and I was looking for monetization techniques outside the typical ads. Disqus Discovery seemed like the right place to start.
What is Disqus Discovery?
“Increase your traffic and make money from your website’s engagement with the new Discovery box.” -Disqus
Basically, the Disqus commenting system just adds an extra section in your comments area that includes “related links”
How Disqus Discovery hurt my rankings?
After implementing it, I was fairly happy with the layout since it provided a non-intrusive presentation of ads. It was a somewhat nice layout and straightforward presentation that just seemed too good to be truth. It was. After four days of implementation, I decided to take a look at my traffic stats (I was busy with some clients, normally I check every day). To my horror, traffic to my main site drastically dropped. Not only that, my rankings with keywords related to my industry were dropping like the great depression. I was terrified.
There were no relevant news about a Google update and I keep my websites fairly white when it comes to search engine optimization. No suspicious activity was detected in my servers, I was not hacked, and my number of backlinks was the same. No reports in Google webmaster tools or anything. The only thing that changed was the implementation of Disqus Discovery Ads. Also, I was used to just publish an article and have it picked up by Google in just minutes, all the articles that I had published ever since take considerable more time to be indexed.
Why monetizing my site hurt my rankings?
There is no a clear explanation why Google decided to fround upon my rankings after I implemented Disqus Discovery, yet in my experience with SEO something that gets this kind of Google hate is unrelated links. And God I found a lot.
I went to my website and with my Chrome NOFOLLOW extension verified that Disqus was adding unrelated or poorly related linked content to my site. Not only that but the content was draining my Page Rank due to the fact that is was DOFOLLOW links.
Solving this issue
I deactivated Ads Discovery and just allowed comments in my website. I saw a near instant improvement as soonest the Googlebot visited my site. Disqus should take care of this issue by marking up the ads and adding nofollow tags automatically to help website owners stay relevant. Otherwise websites with this kind of monetization might drop in rankings.