Google Has Officially Penalized Rap Genius For Link Schemes
Whilst this may be surprising to some people on HN, this happens all of the time to sites who build links in an unnatural way.For instance, this has happened in the past to well known brands such as J.C Penney through NYTimes expose[1], Interflora[2] more recently and a lots of others.An apology which RapGenius offered [3] doesn't fix this either.Is it fair? Yes and No.The only reason it isn't fair is that the site disappears from Google for the BRAND term e.g. [rap genius]. 
My personal belief is that, devaluing the site for the BRAND term e.g. [rap genius] actually devalues Google's quality. On the other side of the coin, if someone searches for [X rap genius] whilst they are under penalty its fair that they do not rank for that either. However, there are obvious reasons as to why the search quality team have decided to do this.How RapGenius can fix it / How you can too if your site gets a penalty:First of all, RapGenius if they are doing any link building now they should pause it immediately until they’re out of penalty.Secondly, in their apology [3] said:  "With limited tools (Open Site Explorer), we found some suspicious backlinks to some of our competitors"

They don't actually need to use any other tool to get out of penalty beyond Google Webmaster Tools although, ideally they should clean up all the links beyond the ones Google has found (trust me, Google doesn’t find them all within WMTs). Once you get out of a Google manual penalty and get hit by one again the search quality team takes a much closer look – you don’t want that!Anyway, they should download all the links in WMTs, OSE, Majestic etc (although it looks like they only have OSE[3] so they should just download them from WMTs and OSE) and then remove the duplicates.Once they’ve done this, they should flag every single link which, they believe is causing the penalty.After identifying all the links which are causing the penalty, they should create a Gmail to outreach to all of the sites to remove the links. They should outreach to all these sites and documents all the sites they’ve contacted, status – still live/nofollow/removed/requested payment/no response etc.Having got some links removed/nofollowed etc, they should then disavow all the other sites that have requested payment or not given them response to the removal. Personally, the disavow(s) that are done by myself are usually done at the domain level although, there are reasons to do this at the URL level as well (Rap Genius needs to make the decision which one to disavow).After submitting the disavow they, should submit a reconsideration request which outlines, the work they have done – from the spreadsheet – and also offer Google’s Search Quality Team the login to the Gmail to show they’ve tried to get the links removed and that some people have asked for payment etc.The Google Search Quality team will review the site then, they’ll either flag more links to be removed or they’ll get out of penalty – after which Rap Genius will start appearing for the BRAND term again and other results once the Google Algorithms trust the site again.[1] http://www.nytimes.com/2011/02/13/business/13search.html?_r=...[2] http://searchengineland.com/google-says-no-comment-on-why-in...[3] http://news.rapgenius.com/Rap-genius-founders-open-letter-to...