Not every site is impacted the same way by Penguin, Google's algorithm that targets spammy link building tactics. On Twitter, Google's Matt Cutts told one webmaster to continue doing backlink cleanup, as the site has a "very mild case of Penguin."
The tweet itself was quite interesting, and seem to be in response to an issue the webmaster brought up to Cutts during a recent conference, as Cutts is well known for writing down webmaster concerns in his ever-present notebook. Cutts initially tweeted about checking on the site, which had been hit by a Penguin issue, and mentioned a manual action was revoked on back in November.
The issue seems to go back earlier than that, because their tweets between Cutts and Chipper Nicodemus date back to the fall when he tweeted the site verticalresponse.com and stating there were issues with backlinks and how Google Webmaster Tools was displaying them.
It isn't surprising to hear that there are different degrees of Penguin. We've certainly seen this in the past.
Some sites get an unnatural linking penalties warning in Google Webmaster Tools, yet see no difference in the rankings. Others get a warning, yet see only specific pages that were linked to be affected. And some sites get the warning and see their site entirely removed from Google, where it doesn't even rank for their company name.