Super Human Trafficking

In a setting where there is a Witch Species, aliens, fairies, or superpowers that show up with sufficient regularity, these Differently Powered Individuals will have the hardship of being hunted by those who want to exploit them for money, power and ...other uses. The government, corporations, Mad Scientists and criminal organizations may seek to enslave and co-opt them to evil ends, such as spying, Super Soldiering, For Science!! and many other purposes.

In extreme cases they may become a Slave Race or Endangered Species thanks to this Fantastic Racism. The protagonists are likely a part of this oppressed group, and have to spend the story on the run from their oppressors, trying to escape their captors control, and/or thwarting their plans and helping their fellows escape. As a result of this trope, members of this oppressed group are likely to choose Transhuman Treachery and the enslavement (or eradication) of mankind, which can be poetically tragic if the fear of this is what lead to the enslavement in the first place.

This has some basis in Real Life. The Industrial Revolutions (there are two of them) deserve most of the credit for ending slavery, particularly in America. Although the introduction of the cotton gin in fact prolonged plantation slavery in the South by making cotton a profitable crop which needed many, many hands, the tractor and other farming machines did eventually help reduce the need for physical labor.

However, in a world with Differently Powered Individuals, assuming that these powers are significant enough to upset the balance of order, you've once again made slavery a relevant business. Conceivably, finding a way to make these superpowers universally available via Super Serum would act as a "third" industrial revolution in this case.

Anime

 * In One Piece, Fishmen inherently have 10 times the strength of normal humans, but they are constantly getting captured and placed into slavery, where they are bought for extremely high prices by the fabulously wealthy.
 * Witch Hunter Robin had the inquisition out to mostly kill witches, but the Japanese branch wasn't averse to recruiting witches... in order to use them to hunt down their own kind. The ones they captured were then enslaved (or processed, it's not clear) to produce "orbo," an Anti-Magic material.
 * Darker than Black Contractors were treated like dangerous, though useful monsters and either used as expendable killers or experimented upon at will — at least, until U.N. intervened... to demand that countries share this research and form PANDORA. Dolls who got a shorter straw were treated like corpses with still living brains: if normal humans don't take cyborgization well, try to cut off a Doll's legs and "program" him to test the replacement. Just like that, it's equipment. Or sometimes a pretty one get "programmed" and sold as a Sex Bot — it's considered illegal, but behind the Masquerade there's very little difference.
 * The manga series +Anima is about young people who develop the ability to transform into Petting Zoo People, with the ability to grow wings, claws, tails, and more. Discrimination against the +Anima occurs in many places, but in Sailand, enslaving them is legal and there is an active business. It's implied that they're usually sold to people who can make the most use of their abilities, (such as a fisherman who wants to use a swimming +Anima for his work) though attractive +Anima may be sold to rich people and artists for the purpose of standing around and looking pretty.

Comic Books

 * The 1970s alien version of Starman spent years as a drugged slave being bought and sold by various "collectors".
 * At one point, Fantastic Four foe the Puppet Master attempted to sell a number of Marvel Comics superheroines under his Mind Control as Sex Slaves to various nasty sorts.
 * 1980s Justice League of America villainess the (human) Queen Bee was introduced running an auction to sell off a brainwashed superhero from another world.
 * In the Silver Age and in the 1990s the original alien version of the Queen Bee has sometimes tried to transform the Leaguers into her "drones."
 * Justice Society of America enemy Roulette engages in this so that she can profit from betting on superhuman blood sports.
 * The Cyborg-Superman and Mongul have both tried to do this to the members of the Green Lantern Corps.
 * The X-Men are basically the Trope Codifiers. Among the groups out to enslave them are: The Weapon X project, the U-Men (although in this case, they were specifically trafficking mutant body parts, blood and whatever else carried the mutations) and the island nation of Genosha, which built its prosperity on mutant slavery.
 * X-Men villain Mojo's entire existence is practically to televise Differently Powered Individuals doing awesome things for the benefits of higher ratings. Their consent, is of course, purely optional.
 * We once did see the Hellfire Club having an actual superhuman auction. This isn't as suicidally dumb as it sounds, as the Marvel Universe has always had a population of lower-level superhumans - not always visible, but there. The club wasn't selling anyone who could kill you with their brain. Natch, the X-Men had to break it up.
 * In the DCAU, Superman, Batman and Wonder Woman were once captured and auctioned off to the highest bidder. All the major villains of the DCAU were invited to the auction.

Film

 * In a variant, the alien Prawns in District 9 are used as slaves by their human antagonists.
 * In the original Escape to Witch Mountain Tony & Tia are chased by a Corrupt Corporate Executive who wants to use their powers for his personal gain and a mob of people on a literal Witch Hunt. Not that they know what they'll do with them once they catch them.
 * The Marvel Cinematic Universe has a solitary example: The Incredible Hulk, whom General Thunderbolt Ross says, in no uncertain terms "is property of the US Government". Specifically, since Banner tested an attempt to reverse-engineer a super-soldier serum on himself, the power of the resultant Hulk Out is seen by Ross as useful to the government as study. He's prepared to capture Banner and use him as a guinea pig/monster on a leash for the rest of his life.
 * This is the premise of Push, all the world's superpowers hunt down... people with actual superpowers, killing, brainwashing, and experimenting on them.
 * While never shown at the forefront, analysis shows that Toons in Who Framed Roger Rabbit? are a minority race, corralled into the ethnic neighborhood of Toontown. This is due to Judge Doom's discovery of Dip, the only thing that can harm a Toon, but it utterly wrecks them in even the smallest quantities. This allows Doom to rule Toontown with an iron fist and pick off any insubordinates.
 * The entire plot of the Deadpool movie is driven by the fact that an unnamed group of villains has discovered a scientific process for triggering latent mutations in people with the right genetic potential. So they find people with the right genes who are already in desperate life situations, wave profitable recruitment offers at them, and get them into the laboratory... and then imprison them, torture them, break their wills, mutate them, fit them with "control collars", and then sell the resulting lobotomized 'super-slave' to Third World dictators, arms dealers, crimelords, and whoever else has a sufficiently large pile of money, a profound lack of ethics, and a job opening for a super-powered enforcer and killbot.

Literature

 * In Crest of the Stars, the Abh were originally created to be slaves. Now that they have an empire of their own, they're hated.
 * In The Dresden Files, immediately after the events of the novel Changes, a group of aquatic supernaturals known as the Fomor start snatching up humans possessing varying degrees of magical talent. In the short story Aftermath, Murphy has to disguise herself as a kidnapper selling a couple of werewolves in order to track down and destroy a Fomor group operating in Chicago.

Live Action TV

 * This is the ambition of the Doctor Who villain Henry van Statten. Pity his first attempt involves a Dalek.
 * Heroes had a mix of both options by the same organization, which both hunted, exterminated, recruited and blackmailed people with abilities.
 * In Firefly, psychics are taken to a lab known as "The Academy" at young age where The Man experiments on them to create Super Soldiers. Any escapees are hunted by "Hands of Blue" agents.

Tabletop RPG

 * In the Aberrant role-playing, some novas (superpowered individuals) are hunted by criminal syndicates who kidnap them and harvest their organs to make superpowered drugs.
 * Champions. The organization PSI (Parapsychological Studies Institute) hunts down and captures people with psionic abilities and brainwashes them into becoming villains and slaves of PSI. PSI plans to use them to take control of the world.
 * In the New World of Darkness gameline Hunter: The Vigil, the Cheiron corporation does this to any being with powers, dissecting them to make medicine. Interestingly their strategy is stated to be very successful at curing the sick. They also harvest organs to give their agents superpowers.
 * Shadowrun. Drakes are creatures which appear to be human but can shapeshift into the form of small dragons, with appropriate powers. Once they started to appear, powerful entities such as Great Dragons and MegaCorps immediately started to hunt them down and capture them.
 * The Great Dragons feel entitled as the ancestors of the Drakes were originally created by the Great Dragons as a slave race of artificial magical constructs. Not that this justifies them now, but you can at least see the train of thought that led them to this decision. The megacorps, OTOH, are doing it because they're just as willing to enslave ordinary humans as they are empowered ones.

Video Games

 * The Harvester gang in Deus Ex Human Revolution likes to kidnap people with augmentations and cut them out to either sell or install in themselves. Not a very nice group of people, all things considered.
 * Biotics (especially untrained children) in the Mass Effect universe are very sought after by illegal groups, particularly if they're powerful for their species. In a more benign variant, biotics are also rare enough among humans that there are monetary incentives offered for them join the armed forces; the discrimination they face is so omnipresent that a very large percentage of them do indeed sign up just to escape it.
 * The Blackwatch of Prototype once infected the entire population of a town with an experimental bioweapon. Every subject died after the town had to be shelled except for two, a woman and her newborn baby, who both exhibited odd capabilities. They were seized and designated "military assets" to spend the next forty years imprisoned and subject to all kinds of tests to develop tactics for fighting (and creating) new bioweapons.
 * Legalized example in Dragon Age: all individuals, human or elf, with magical talent can be taken away by the Templars and placed inside a glorified prison with others of the like (ostensibly for their own and everyone else's protection) to toil away for the Chantry and whomever the Templars deem suitable clients.
 * Two things of note: the mages get to share in the revenues that they generate (indeed, in many places like Ferelden the mages seem to receive the lion's share), and the 'all mages are indentured by the Church' scheme is actually a historical compromise position -- the fallout of the Andrastian Rebellion vs. the Old Tevinter Imperium had left mankind torn between those who favored mage supremacy and those who wanted mage genocide, until the Chantry and the Templars proposed a third option.

Web Comics

 * In Drowtales, while "Goblin" races (humans, orcs, etc.) are terrified of Fae races (elves, faeries), one kingdom has offered a reward for captives of elven blood
 * In Blue Yonder, the Davenports have been targetted. Their parents were taken in the Backstory, and Maiden Flight sacrificed herself to buy Blue Yonder time -- and the reasons why are as yet unknown.
 * Paranormal Mystery Squad even participates in this for a while - at the level of goods collection, of course.

Web Original

 * One Global Guardians PBEM Universe story saw the heroes shutting down a slaver ring who were selling female Pelkons (a race of very human-like alien refugees who had been stranded on Earth during the Xorn invasion of 1985) into sexual slavery. A partial subversion in that the Pelkons have no "superhuman" abilities to speak of.

Western Animation

 * DC Comics villainess Roulette turns up with this M.O. on Justice League as well (see comic books above).
 * In Young Justice, the "genomorphs" are this: genetically-engineered/cloned superbeings that are kept under mental control until ordered with a task. In fact, the pilot was a carefully-crafted revolt by the genomorphs to supplant the control of The Light (the Omniscient Council of Vagueness which created them) and allow the most human-looking of them (Superboy) to escape and act as their advocate to the outside world.
 * Unfortunately, the Light is still in control, just more subtly, and Superboy has trouble even advocating for himself. Also, they left the same guy who was brainwashed into being head of security for the evil version as head of the reformed version, instead of getting him some damn therapy.
 * In Fairly Oddparents, Fairy's are often hunted, almost always Mr. Crocker going after Timmy's fairies.