http://tardis.wikia.com/wiki/Great_Intelligence
Not exactly a nobody villain, but for something that supposedly pre-dates the universe, you'd think its final FU to the Doctor would be something a little cleverer than "Gather lots of people who would give their life to save the Doctor in the one place they can do that."
Regarding the Mystery Doctor, I don't understand how he never showed up in Clara's journey through the Doctor's life just because he did something 'not in the name of the Doctor'. Except, then, he does show up. Because ????.