Nintendo sent over this statement to us just now...
As part of our on-going push to ensure Nintendo content is shared across social media channels in an appropriate and safe way, we became a YouTube partner and as such in February 2013 we registered our copyright content in the YouTube database. For most fan videos this will not result in any changes, however, for those videos featuring Nintendo-owned content, such as images or audio of a certain length, adverts will now appear at the beginning, next to or at the end of the clips. We continually want our fans to enjoy sharing Nintendo content on YouTube, and that is why, unlike other entertainment companies, we have chosen not to block people using our intellectual property. For more information please visit http://www.youtube.com/yt/copyright/faq.html
In other words, Nintendo has ads running on fan-made Nintendo videos that hit a certain length or feature certain content. Thanks to Nintendo for the comment!
Update - Our friends at GameXplain bring up an interesting point. The blurb above from Nintendo 'doesn't mention that it cuts off all revenue to the creators of any claimed videos.' Apparently that's the situation, with GameXplain already being impacted. To clarify, 'it's only for the claimed videos' right now, but that could change.