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Found this post (from a recent Chaos Computer Congress 30C3) on hacking the microcontroller embedded in the actual SD cards. I'm not sure if it'll actually lead to anything or how to begin trying, but, having custom microcontroller code running inside the SD card in the 3DS sounds interesting.
http://www.bunniestudios.com/blog/?p=3554
That's one hell of a find. That's something that could be significant for just about any device that reads from an SD card.









