Rape was, according to the Seventh Doctor disguised as John Smith, non-consensual sex, usually effected through violence. (NA: Human Nature)
In AD 62, Celtic Queen Boudicca rebelled against the Roman Empire when Roman agents raped the women of her kingdom. Her rebellion was swift and brutal: the offending Romans were, according to John Smith, "skinned alive and impaled on posts with their intestines . . . in their mouths". (NA: Human Nature)
During an incident in the village of Sair, Peri Brown had bedded with Tablibik whilst under his spell. The spell in question was the sole cause of any sense of desire Peri had torwards him, meaning that any sexual acts that they may have engaged in that night could not have been considered consensual. (VD: Fascination)
On 28 March 1963, 17-year old Lizzie Lewis was raped and murdered on the way home by Ed Morgan, the man whom she had just been to a dance with. (TW: Ghost Machine)
Dodo Chaplet was nearly raped by one of her fellow patients at the Glasshouse, probably in 1966. She cried out for help, but neither her fellow patients or the facility's staff would assist her. Instead, she had to defend herself against his violence. To stop him tearing at her gown and trying to force himself on her, she kicked him in the face. He stumbled backwards, and cracked his head on a table. Her would-be rapist died within a matter of moments. (MA: Who Killed Kennedy)
Sometime around 2006, Oswald Danes was convicted in Kentucky of raping and murdering a 12-year-old girl. (TW: The New World)
It is implied Vasor attempted to do this to Barbara. (DW: The Keys of Marinus) It is also heavily implied that the viking invaders raped Edith. (DW: The Time Meddler)
The Eleventh Doctor was nearly raped by has companion, Amy Pond, but managed to stop her.(DW: Time of Angels)
Behind the scenes
According to The Brilliant Book 2012, a book that contains non-narrative based information; in the 19th century, a group of Chinese criminals attempted to rape Jenny, but were stopped by Vastra.
