Ralph_Slate - 2:43 pm on Aug 10, 2012 (gmt 0)
I too am worried about this phenomenon!
My site is viewed as a very trusted resource, and because of this, I have 88,000 links (that's not a typo) from Wikipedia. Wikipedia has essentially built a ton of their pages by pulling the information from my site. All the links are nofollowed (so I get no juice from Wikipedia), but the main problem, as you describe it, is that so many spam sites scrape Wikipedia and republish on their own sites, and the links go along with it.
I am seeing that about 60% of my daily "new links" in WMT are from these spammish sites. Yes, they are still nofollowed, and thus supposedly removed from the graph, but what if Google is tracking nofollow links in their penalty algorithm in an attempt to punish forum spammers?
I saw a significant drop in Google referrers on April 24 (about 50% to 80%). Although I have been in considerable disagreement with a particular user on the Google forums (who also frequents these forums), as to whether the effect was Penguin or Panda, I have to believe that the date makes it more likely that it was related to Penguin, not Panda.
John Mueller made the statement to me, in the forum, "I don't see any general issues with the links to your site", and suggested that I need simply make my site "the best site of its kind". Because of that one of the moderators now forbids me from discussing links in any way, however I still think that Mueller was simply referring to the fact that I don't have a manual link penalty on my site. I don't think he can do algorithmic analysis so easily.
I feel like my site's domain authority has been penalized, and because of that, pages on my site which do not have any backlinks, but are still the authority on the obscure subject, are not being returned as much by Google. It is not uncommon for me to search for a particular topic on Google - where a page on my site would satisfy the query - but my page isn't coming up, and none of the pages returned satisfy the query either. The same queries on any other search engine return my site as #1 without fail.