This story has popped up and has lead to some interesting discussions, so why not discuss it here?
Nintendo has become a Youtube partner and registered their copyright stuff with Youtubes content ID matching codemagics. What this means right now is that if you have a video on Youtube over a certain length that contains Nintendos stuff, like a Let's Play, and you currently make money off that video by being a Youtube ad partner...then your free ride is over. Your video will remain up but an ad will be place before, after, or on the side of your video and Nintendo will be taking the money earned from those ads, not you.
This has upset the LP community and has led to some interesting discussions on what constitutes fair use. Video reviews, short videos showing a specific section of a game as a tutorial or to criticize shouldn't be affected. This is really a move to target the long Let's Play videos that can end up showing an entire playthough of a game. Should those be allowed? Even if you're offering comment on the game as you play, you are still broadcasting the art and music (all copyrighted) of the game.
There is also the claim that it is free advertising for Nintendo. I think that misses some key points such as...does Nintendo even want it? Do they care? A game like Minecraft got big because people show what they can make in the game, the youtube videos were very important for its success (Mojang turned down Youtube when they were offered the same deal). I don't think the same can be said for Mario Galaxy. If people are watching the videos to decide to buy them then what does showing an entire playthrough get you that something like a Giant Bomb Quick Look doesn't? And for certain games I can see a whole playthrough video damaging sales. What would playing Uncharted 3 really offer me over watching a Let's Play?
So, I dunno. I can see why this would be upsetting to the makers of these videos but I don't think what Nintendo is doing is really wrong. They aren't pulling videos off youtube and this would only affect the long videos that probably fall outside of "fair usage".