YouTomb is an interesting project by MIT Free Culture that collects YouTube videos taken down because of copyright infringements. "More specifically, YouTomb continually monitors the most popular videos on YouTube for copyright-related takedowns. Any information available in the metadata is retained, including who issued the complaint and how long the video was up before takedown. The goal of the project is to identify how YouTube recognizes potential copyright violations as well as to aggregate mistakes made by the algorithm."
Since YouTube operates under Digital Millennium Copyright Act, it's obliged to take down content if it receives a notification claiming infringement from a copyright holder. In some cases, videos are wrongly taken down because YouTube is in no position to judge the validity of a claim.
According to YouTomb's stats, the companies that have recently taken down the biggest number of popular YouTube videos are: TV TOKYO, Viacom, Warner Bros, World Wrestling and other media companies. "YouTomb is currently monitoring 157340 videos, and has identified 4389 videos taken down for alleged copyright violation and 13330 videos taken down for other reasons."