The ancestral Native American tribe to which Chakotay belonged at one time suffered frequent rape by "white conquerors". One of these rapes produced Ce Acatl, a great leader of their tribe. (VOY: "Basics, Part I")
In 2267, during Festival on the planet Beta III, when the inhabitants would lose their inhibitions to violence, rape occurred openly in the streets. Once the clock struck red hour, Kirk and the landing party from the USS Enterprise immediately witnessed men chasing after women. First, they saw a man grab a resistant woman across the street from them, and shortly afterward Bilar was seen dragging Tula away by her shoulder or hair. While running to seek shelter from the chaos, the landing party passed a man with white sleeves who was carrying a struggling woman over his shoulder. Shortly afterward, from the safety of a second floor window, Kirk saw the image of a man assaulting a woman in silhouette, and heard the screams of other women. Later, when festival was complete, Reger consoled a screaming, emotionally distraught Tula who had returned from Festival heavily traumatized by her experience with Bilar. (TOS: "The Return of the Archons")
Shinzon's telepathic interaction with Troi through his Viceroy in Star Trek Nemesis was presented in the context of rape, similar to Troi's experience of telepathic memory invasion with the Ullian Jev in "Violations". Troi also experienced something akin to rape in "The Child" where she was impregnated against her will in her sleep.
Tucker's impregnation in "Unexpected" can be considered rape, as he was deceived by Ah'len, the Xyrillian engineer into believing that their form of reproduction was simply a "game" he was being invited to play.
Some legal definitions of rape include sex under false pretenses, such as Dukat's having sex with Winn Adami while pretending to be a Bajoran in "'Til Death Do Us Part". This concept is not universally recognized, and was not mentioned in the episode. Please see Wikipedia's article on Rape, linked below, for more information about how the term is defined.
In the Star Trek: Deep Space Nine - Millennium novel Inferno, Arla Rees (β), a Bajoran Starfleet commander, experienced a Pah-wraith induced hell where, during the Occupation of Bajor, she was tortured and raped by the Cardassians for days before being killed, and then forced to "relive" those events again and again.