Two people are coerced into sex by a third party. This can be part of a Sadistic Choice—wherein the villain will threaten one or both of the victims with bodily harm, unless the two cooperate—or it can be under pure coercion from one who is more powerful or manipulative.
This is handy for a villain who doesn't like to get his hands dirty. It also lets him use his victims against each other - making it very efficient. Maybe watching gets him turned on. So maybe he does join in a little later.
An extra dimension of angst can be added when two characters have deep feelings for each other, but those feelings are not sexual in nature (e.g., friendship or platonic love); alternatively, they may have latent romantic feelings, but exhibition is not how they would have wanted to express it. Judging by the examples below, it's also disturbingly common for the pairing to be incestuous.
It can be heartwrenching, especially when the victims struggle to comfort each other in the midst of the mutually traumatic ordeal, or suffer the perversion of their honest affection. It can also be an Excuse Plot for pointless titillation.
Compare/Contrast Sex by Proxy. One might expect Aliens Made Them Do It to be the Sci Fi counterpart, but in fact that trope is much Lighter and Softer, often played for laughs or a light-hearted Ship Tease.
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Anime and Manga
Robotech has an episode where Hikaru/Rick, Misa/Lisa, and Hayato/Ben are captured by the Zentraedi and ordered to demonstrate human procreation. Because the Zentraedi are completely ignorant about sex and are hugely disgusted by acts of intimacy, the first two manage to get by with just a forced kiss instead of forced sex. (And it's implied that this is Hikaru/Rick's First Kiss, even.)
In Fushigi Yuugi Nakago sends Tomo to seduce away Miaka's Virgin Power after finding himself unable to do so. Tomo opens a clamshell, and implants False Memories into Miaka of marrying Tamahome this time, Tomo disguised as Tamahome. By the way, Tomo is gay, but he complies because Nakago (whom he has a crush on) asked him to do it.
In Irredeemable, the Plutonian is shown forcing a man and woman to make love while roleplaying as him and a former lover.
In a controversial story, a villain called Sleez was heavily implied to have forced Superman and Big Barda to make a pornographic film using Mind Control. Word of God has said that nothing was confirmed, so the truth is up to the readers.
Happens in Fables when Bluebeard uses magic on both Snow and Bigby to make them leave town and spend a week in the woods together, where they have sex and Snow is later shown to be pregnant. They wake up in the woods with no memories of the past week, and when they realise they had sex Snow at first accuses Bigby of rape, until he points out that for all they know she was the one who instigated it, when in reality they were both effectively raped by Bluebeard since it was his magic that took away their ability to consent.
In Hinge of Fate by ramos, Snape and Hermione are forced to do this when the latter is captured by the Death Eaters. It's presented as the lesser of two evils, with Snape being the best choice to perform the act. It is implied others would not be as gentle.
ThisStar Trek: Enterprise fanfic, pairing Malcolm Reed and Trip Tucker. Notably, the author deals quite well with the problems this creates between the two, as their mutual attraction meant they enjoyed it but the feelings of violation were still there, and it takes them quite some time to untangle the two.
In the Pony POV series, this happened with Filthy "Onyx Tiara" Rich and his household staff, under the influence of Discord. While Filthy was discorded, anypony he touched (even the one male member of the staff) turned into an imitation of his wife, and, well... Yeah. And of course, they all remembered what happened afterwards. It is unfortunate that the goat-faced creep responsible cannot be permanently dealt with.
In Sephirothslave's story Shinra High SOLDIER, Jenova takes control of Sephiroth and forces him to rape his fiancee Julia.
In the appendix of the TouhouDark FicA Scarlet-Stained Memoir it is mentioned that Nathaniel was raped by Meiling on the orders of Remilia Scarlet.
ThisStar Trek: The Next Generation fanfic, which has Picard conduct a diplomatic mission, for resources the Federation needs, with a species that has institutionalized degrading, rape, and prostitution of their women, even whoring them out to diplomatic agents that visit their planet. Picard is offered one such woman, named Yanet, and despite his objections to the matter realizes from her own testimony that refusing to have sex with Yanet would hurt his mission and would cause them to beat her savagely if she failed to entertain him. Forced into a corner Picard has sex with Yanet, and through continued interaction with her learns that she's actually Q who has lost her powers and has been trapped on this planet as punishment. Since Q knows of an alternative way of getting the resources the Federation needs Picard makes it his priority to rescue her, something he eventually succeeds in doing.
Se7en has an extremely violent and disturbing example. As always in this movie, we see only the aftereffects. It also results in Murder by Proxy.
The 2009 Mexican film Daniel and Ana, which falls somewhere between Based on a True Story and Based on a Great Big Lie in its graphic nature, concerns a brother and sister whom pornographers kidnap and force at gunpoint to have sex with each other on camera.
In the movie Primal Fear, the main character discovers a home video owned by the murdered archbishop, in which the archbishop forced two altar boys to have sex with a girl on camera.
In Eastern Promises, henchman Nikolai is forced by his boss' son Kirill at gun point to have sex with a prostitute.
Kirill: YOU ARE GOING TO FAHK ONE OF THESE BEETCHES!
In Swordfish, Gabriel forces Stanley at gunpoint to hack into the mainframe of the United States Department of Defense, while he gets a blowjob from a woman who works for Gabriel. Afterwards Stanley is more pissed off about the gun to his head than the fact that he was forced into sex, partly because the film implies the "Not If They Enjoyed It" Rationalization.
Shards of Honor: Vorrutyer orders Bothari to rape the prisoner of war Cordelia Naismith. This is a common enough order from Vorrutyer to Bothari that Vorrutyer does not expect to be disobeyed.
In Mario Puzo's The Familynote Not that family, Rodrigo Borgia forces his son to deflower his daughter, believing that a woman will forever be loyal to the man who takes her virginity.
In White Midnight by Dia Calhoun, Mr. Brae wants an heir to his estate, so he forces Rose to choose between sex with him and sex with his son Raymont (who also has no choice in the matter, and is widely rumored to be a hideous monster). She chooses Raymont and eventually has his child, but she's not happy about either option. Oh, by the way, Rose is fifteen, and Raymont is maybe seventeen.
It is revealed in back story that Tyrion once married a prostitute, but the marriage was ended when his father Tywin found out about it, and as punishment Tywin made Tyrion watch as his guards raped her, finally forcing Tyrion to go last. This becomes arguably even worse (if only because Tywin deceived Tyrion in the process) when we find out that she wasn't actually a prostitute; she was what she claimed to be, a cobbler's daughter met by chance on the road. This is generally considered to be Tywin's Moral Event Horizonand directly leads to his death when Tyrion finds out that she was not a prostitute.
Also, on more than one occasion Ramsay Bolton forces "Reek" a.k.a Theon Greyjoy to perform assorted unidentified things with Ramsay's thirteen-year-old bride Jeyne Poole.
In Frostflower and Thorn it is necessary to strip a sorceron of his or her powers in order to safely touch him. Since sorcerous powers are tied to virginity... well, you do the math. Due to the risk involved this work is often relegated to understandably reluctant hirelings.
The same goes for Diona, who is forced to have sex with Rhaskos who was specifically picked by Cossutius because of his questionable hygiene.
Early in Blood and Sand, the gladiators are commanded to have sex with the slave girls for the viewing pleasure of the visitors of the ludus. Basically, it's porn for people without TV.
The murderer in the Criminal Minds episode "Compromising Positions" had this as part of his MO.
In Season Six of True Blood, Jessica is held captive in a vampire testing facility where she is told to have sex with a vampire named James or else both of them will face torture. All in the name of science, of course. Though Jessica gives her very reluctant consent in order to make things easier for James, he ultimately cannot bring himself to rape her and is burned with a UV light for his trouble. (The two later bond over their traumatic experience by having consensual sex. Because this is True Blood.)
In season one of Skins, a bunch of guys tried to force Tony to rape his sister (who was unconscious from a drug overdose at the time). They actually weren't planning on making him do it, though, they just wanted to scare him, which they succeeded at quite spectacularly.
Law & Order: Special Victims Unit had a case where a boy was born with a twin brother, but the brother's circumcision was botched, mutilating him, so the doctor's "fixed" it by doing a sex change operation at the parent's request. The parent's raised the child as a girl with the help of a psychiatrist who strongly believed that with the proper Nurture they could overcome Nature. To try teaching the "girl" to be a girl the doctor used "her" brother to teach "her" her part in a physical relationship by putting them into the positions (though there never was penetration), while they were still in Junior High.
In another SVU episode a pair of spree killers would attack groups of people and force the men to rape the women, and then to rape each other before killing them. Even the seasoned sex crime detectives who deal with "ordinary" rapists and paedophiles virtually every episode thought these killers were worse than what they were used to.
A storyline on Nip/Tuck had the elderly husband of the woman Christian was currently bedding demanding that they have sex in front of him. He was unable to have sex due to his age and health problems but still wanted to get off on seeing her get off and decided to use her affair with Christian to his advantage.
In the 5th season of Sons of Anarchy, Carla forces Gemma and Nero at gunpoint to have sex in front of her. She did this out of jealousy, since she had an unrequited crush on Nero (who it turns out is in fact her half-brother). Gemma and Nero start, but refuse to go along with it when Gemma breaks down crying. Carla then shoots herself.
In Season Three of Shameless US, Terry Milkovich catches Mickey and Ian having sex in his house. He beats them severely, then calls a Russian prostitute and forces Mickey to have sex with her and makes Ian watch. He does all of this at gunpoint.
Metal Gear Solid: Ground Zeroes gives us a very chilling example that's thankfully relegated only to an Audio Log. Skull Face, the Big Bad, forcing Paz and Chico to have sex with each other in front of him as part as their vicious Cold-Blooded Torture. This serves the purpose of completely breaking Chico, who finally spills the beans, ratting out Big Boss and the MSF, leading to the tragic climax of the game. Made even worse by the fact that Chico is very much in love with Paz.
In Dominic Deegan, Stonewater's rape of Melna (as opposed to letting the host tribe execute her) was clearly meant to come off this way. Too bad nobody told them: for years Melna blamed Stonewater and Stonewater blamed himself. Melna eventually figured it out in the rebirth of Maltak arc, and killed the guy responsible.
In Futurama, the probe "V-Giny" forces Leela and Zap to have sex to reenact Adam and Eve.