While not precisely a villain, Mary Whitehouse almost deserves the title for she has dogged the Doctor's steps with her campaigns against violence in British television since the sixties, frequently targeting Doctor Who specifically. Mary Whitehouse was always attacking the programme for being too frightening. She once called it the most violent show on television
Taking over in Season 12, the Fourth Doctor's stories instantly became much darker and more horrific than anything which had preceded them, fighting against the giant insect Wirrn, shape-shifting Zygons, ancient mummies, human-hating Robots of Death, knife wielding dummies in Victorian London as well as the evil creator of the Daleks - Davros. However, the new-found emphasis on terror brought the show to the attention of a foe he was destined to lose against - Mary Whitehouse and her powerful and deadly National Viewers and Listeners Association.
Doctor Who had come under fire from Mary Whitehouse and her National Viewers And Listeners Association before, but never to the same degree as after the broadcast of part three of Deadly Assassin on November 13th, 1976. Whitehouse protested strongly about several sequences in the surrealistic, nightmarish episode but none more than the freeze-frame shot of the Doctor's head being held under water for several seconds. Whitehouse even quoted one child who had allegedly told his mother that he would do the same to his younger brother the next time he made him mad. Unlike past complaints by the NVALA, this time the group was successful in coaxing an apology from BBC Director General Sir Charles Curran. Indeed, the BBC even edited portions of the offending scene from the master tape of the episode, meaning that the BBC no longer holds a complete copy of part three. Fortunately, the sequence is preserved in its entirety on prints made for international distribution.
This would be the last major public outcry by Whitehouse against Doctor Who, but also marked the start of a general reduction in the horror content of the series and it's decent in silly comedy. Some fans attribute show's growing unpopularity which eventually led to it being taken off the air in 1989 to this change in direction, so ultimately Mrs. Whitehouse's campaign may have been successful, which would make her the only villain to have actually defeated the Doctor.
Mary Whitehouse died after a long illness in November 2001, at the age of 91