6. The Silence
Nine had the Slitheen, Ten had the Weeping Angels, and Eleven had the Silence. Moffat did an amazing job at creating such a creepy villain, beyond the creepiness of the Weeping Angels or anything he made before. He made a villain who created a religion whose followers were all out to get the Doctor, and kill him. Its astounding what these creatures did to Eleven the religion the Silence started unknowingly took Amy away from them for most of season six, and then showed us where River had come from. Moffat didnt just make evil villains intent on destroying the Doctor physically, he made villains intent on destroying the Doctors everything. There are the monsters that we see (or do we see?) and then their religious order. So really, there were two villains to battle in season six the religious order took a baby from one of the Doctors best friends, and raised her to be his own bespoke psychopath, and then, despite the fact that River had fallen in love with him, she still had to kill him. This wasnt youre average old antagonist, this was something that pulled on every single one of your heartstrings and made the view ache for any possible other way. The Silence were interwoven in series six, and every time you thought you got away from them, another story arc would come up and happen. This wasn't done in a way that made the viewer tired of them, because the Silences story was never finished. They were never defeated, and to this day, I still believe that, if Moffat wanted, he could bring the Silence back.