Pointy-Haired Boss: Look what one of our engineers said to a reporter! Catbert: [reading newspaper] "Our technology is putrid, but we compensate by ignoring complaints." Pointy Haired Boss: You know what would be more fun than fixing those problems? Catbert: WITCH-HUNT!!!
A search, often misguided, for hidden enemies of the community.
There is a menace in this community. They may look like us, but they are not us. They lurk among us, waiting for their chance to do us harm. Anyone could be one of them: your neighbor, your friend, even a member of your family. But don't be fooled, they're only pretending to be your loved one. In reality, they are a witch/Jew/child molester/Communist/devil worshipper/Shape Shifter! We must root out this menace and destroy them, no matter what steps we have to take. After all, the community's safety is far more important than niceties like civil rights and due process, right?
A trope that came into its own in The Fifties as a metaphor for paranoia about Communists in the United States. A community believes that some of its members are secretly enemies in disguise, and attempts to find out which. Hysteria rises, often due to one or more people trying to take advantage of the fear for their personal grudges or advancement. Inevitably, innocent people are accused, often dying or having their lives ruined.
Turns the community into All of the Other Reindeer, and often includes a Torches and Pitchforks scene, and when the target is "witches" can lead to the so-called witch getting burned at the stake.
A frequent "twist" is that the person doing the most to urge on the Witch Hunt is actually one of the enemy group, knowingly (in which case he's conducting it to get rid of his rivals or to spread chaos among the populace) or otherwise (Tomato in the Mirror).
Today, the Witch Hunt has become synonymous with any wild, unfounded hunt for a nebulous 'enemy', in which actual evidence, if such exists in the first place, is scarce. The careers of many prominent people have been broken during Witch Hunts.
Compare Ten Little Murder Victims and Hero with Bad Publicity.
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In Hellstar Remina, a scientist who discover a new planet names it after his daughter, Remina. The girl in question quickly becomes a celebrity (...for some reasons). But when the planet start moving towards Earth at light-speed, eating other planets and stars on the way, some cultists use the panic generated to turn the whole world against her, saying that sacrificing her and anybody who would help her would stop planet Remina. At one point, one of the cultists is revealed to have a tongue similar to the planet's, but it's never developed or explained.
In Rebirth, it's more like "Vampire Hunt" for poor young Deshwitat L. Rudbich, a half-vampire with a vampiric father and a human mother. During the 17th century, he lived a normal childhood until Captain Maybus, leader of the Knight Templar Sacred Knights, stormed the Rudbich Castle. Falling into obscurity, the Captain targeted the family, who hadn't committed any crimes,as a target to re-establish himself. Forced to watch his mother beheaded and father burned in the morning sun, Deshwitat barely survives with the help of the captain's son, Kalutika (whom would later become both his closest companion and then the Big Bad). After that, his life can be summed up as going From Bad to Worse.
A Skrull impersonating Captain America tried to spark one of these by claiming that the Skrulls had been far more successful in infiltrating American society than they actually had been. He knew that if Cap, the most trusted hero in the Marvel Universe, said it, people would think it was true and follow the Star-Spangled Avenger's advice to root out those who were different or suspicious-acting.
He had good reason to think the plan would work, given the Marvel Universe's history of anti-mutant hysteria. Oddly, the X-Men books have hardly ever used the "mistaken identity" part of the trope, instead having the Witch Hunt focus on actual mutants who don't happen to have any dangerous or useful powers, and are thus easy prey.
Then there was the Secret Invasion event, where Skrulls had infiltrated Earth's superhero community. Though while there was rampant suspicion and paranoia, things rarely went further than that and an actual Witch Hunt was averted for the most part.
In No Way Out, the Red Scare of the 1980s is used to set up the dramatic hunt for a supposed Soviet mole as the scapegoat for U.S. Secretary of Defense David Brice, who just murdered his two-timing mistress for cheating on him and needs a patsy for his crime. As it happens, Commander Farrell, the man hired to investigate, knows that he's the man Brice's mistress was cheating with and has therefore been Hired To Hunt Himself. While he ends up exonerating himself of the murder, the Twist Ending reveals Farrell to actually be a Soviet mole.
In The Majestic, the main character is accused of being a communist, ruining his career and nearly driving him to commit suicide.
He did attend meetings of a pro-Communist group in college, although that was because he was trying to impress a girl (who ended up naming him to the committee) and literally had no idea what the meetings were about. An investigator then looked through his script and declared it "Communist trash".
Parodied in Harry Potter and the Prisoner of Azkaban, answering the Fridge Logic of many people who may think "If a witch was caught, wouldn't they use their powers to escape?" about such hunts; with the witches and wizards, using, well, magic. - Harry reads up on history that says any Witch Hunts that genuinely caught a witch and tried to burn them at stake would be fruitless, as the magicians would just use a 'Flame-Freezing' charm to make the fire harmless and only cause gentle-tickling. An individual called Wendelin the Weird liked doing that so much that she let herself be caught 47 times in various alias and disguises, giving Too Kinky to Torture an interesting variation.
Also played straight by Barty Crouch Sr. who started massive witch trials during and after Voldemort's first reign. He prosecuted Ludo Bagman for inadvertently giving a DE spy information, gave the order for Sirius Black to be sentenced without trial, and eventually sentenced his own son to life in prison. Note only one of these three was actually guilty.
In Dan Abnett's Gaunt's Ghosts novel Ghostmaker, Gaunt's enemies Sturm and Gilbear tell the Inquisition of Brin Milo's knacks. Inquisitor Lilith investigates him to see if he's a psyker, Although she knows that his enemies have already tried to murder him and his regiment and are doing this to bring him down. She drags Gaunt in, to shoot Milo if the suspicions are founded. This will allow her to keep Sturm from using it as an excuse to turn the regiment over to the Inquisition, which very few would survive. (Fortunately, Milo escapes.)
Robin Hobb's Farseer books include a specific form of magic, the Wit, which is basically animal-communion abilities and some empathy abilities rolled into one. Witted get all sorts of benefits from their magic, and it sounds as if it would be completely awesome to have... if it weren't for the fact that Witted are treated in much the same way as "real life" witches, blamed for using their magic in completely absurd (and impossible) ways. As it stands, even being suspected of being Witted is enough for a good old-fashioned lynching.
In Rudyard Kipling's The Jungle Book, after Mogwli kills the tiger, the village hunter Buldeo tries to claim the corpse and Mogwli drives him off with the help of wolves. Buldeo believes him to be a witch and the village drives him off, and then goes after his foster parents. Mogwli has to rescue them.
In The Witch of Blackbird Pond, when a serious illness sweeps the town, angry residents begin looking for someone to blame as children start dying. They immediately go to fetch Hannah Tupper, whom the town has always whispered about being a witch. When Kit helps her escape, their anger and accusations turn on her.
In L. Jagi Lamplighter's Prospero Lost, Theo and Miranda discuss the witch hunts; Theo says that many of them were witches, and when Miranda says that records show that many were innocent, she realizes that the Circle of Solomon would have ensured that the records showed them so.
In Silverfall Dove pointed out to one warlike dark elf why an infiltration plot of another drow faction must be stopped as quietly and quickly as possible:
The humans you rightfully distrust will rise to arms in their fear and hatred to obliterate Scornubel, all drow they find, and anything else up and down the Sword Coast that they can call 'drow', or 'friend of drow'.
Inverted in 1635: The Dreeson Incident. Here, the targets of the angry organized mobs are the witch-hunters, along with the anti-Semites. The usual excesses are mostly averted, as the mob has an actual (and accurate) list of names.
Live Action TV
In the Buffyverse, these have been inspired throughout history by the Hansel & Gretel demon. In the episode "Gingerbread", they convince Buffy's own mother to lead a witch hunt that almost gets Buffy, Willow and their friend Amy burned at the stake.
An interesting example in the Angel episode, appropriately titled "Are You Now Or Have You Ever Been". After a man commits suicide, due to a demon who feeds on negative human emotion, the hotel manager and bellboy cover up the crime. Paranoia spreads, with the demon affecting peoples minds, until Angel is hung by a lynch mob of ordinary hotel employees and guests who believed he killed the man. The person who fingered him, a young woman who did so to save herself from going to jail for theft, then spent the next 50 years feeding the demon with her guilt over Angel's "death".
Sort of happened very badly in the second last episode of the first season of Sabrina the Teenage Witch. Sabrina's class went on a Field Trip to a colonial town, and while there, took on the roles of various occupations as some sort of educational thing, though Sabrina lost hers. Just before they started, the tour guide told them that somebody had been given the role of 'witch,' and they would have to figure out who it was. Libby eventually accused Sabrina and put her on trial, but Sabrina used magic to make Libby look crazy and have everybody think she was the witch. Then at the end, the tour guide said that she had lied about there being a witch, in order to prove a point about how hysteria can spread so easily or something. Then at the very end of the episode, Sabrina found her role pack, and her role was in fact witch.
Star Trek: Deep Space Nine had elements of this inspired by the Shape Shifter masters of the Dominion. The fact they keep up the blood screenings even though they know that the guy who came up with it was a changeling and it didn't work on him ...
An episode of Star Trek: The Next Generation saw the Enterprise suffer the near-catastrophic failure of a critical engine part. Suspecting sabotage, and armed with reams of circumstantial evidence, The Federation investigator rapidly begins searching for scapegoats. In the end, it turns out that the part that failed was merely defective, not sabotaged. Unfortunately, the investigator refuses to accept the evidence as presented and utterly destroys the career of a promising young crewman, shortly before she self-destructs by way of a hateful, mindless tirade against a 'suspect'. A note for such villains, don't play political/diplomatic games with Jean-Luc Picard.
After which the visibly distraught investigator comes to her senses, realizes that her entire case has just collapsed because of her outburst, and follows up with a small 'I have nothing more to say'. Surely the best way to end a Witch Hunt.
The Twilight Zone episode "The Monsters Are Due On Maple Street" was a wonderful example: everyone was looking for the aliens among them who were responsible for the power outage, but the real aliens were watching from outside the town. They knew they just had to cut off the power, and the people would kill each other in their witch hunt.
In the remake of that episode, It was a military experiment instead. The soldiers found the results disheartening to say the least.
In the remake of Battlestar Galactica, the military leaders chose not to reveal the existence of human-shaped Cylons for fear of having a Witch Hunt on their hands ("People would accuse their neighbours for not brushing their teeth). When they (later) finally decided to let the cat out of the bag, they set up an "independant tribunal" to initially root out the Cylon infiltrators, but devolved into an Inquisitorial Tribunal trying to pin the blame on whomever they could. Adama shown how different he is than Picard; he did not outwitted the Chief Investigator, he out-Leadershiped her by having her security detail arrest her.
As noted in the Real Life section below, McCarthyism was running rampant in America in The Fifties. Because the show reflects the mindsets of that time, it was a recurring theme on M*A*S*H.
An episode of Charmed has the sisters transport to a Bad Future (a form of Mental Time Travel), where an ambitious man has managed to reveal the existence of the supernatural to the world and has started a nationwide witch hunt, gaining massive political support. They also execute witches by fire, but they do it in a modern way - with automated flamethrowers. The sister manage to undo this by one of them not using a spell on a guy (the same guy who would start the witch hunt) for merely being annoying.
Subverted in a Saturday Night Live sketch depicting a Salem-era witch trial. The sketch makes the expected jokes about it being an obvious Kangaroo Court until the last minute, when it turns out the defendant actually is a witch. He uses his magic to intimidate the court into finding him innocent.
In the Stargate Atlantis episode, "Suspicion," a series of frequent Wraith attacks during expeditions leads the Stargate team to suspect there is an informant to the Wraith among the Athosians living in the city. What follows is what the Athosians would consider a witch hunt with access restrictions and security interviews by the Terrans and they request to move out the moment when land is discovered on the planet. It turns out that there was no spy, Teyla was wearing a Wraith homing beacon that Commander Shepard inadvertently activated when he found it and gave it to her.
In the first-series Blackadder episode "The Witchsmeller Pursuivant," Prince Edmund is accused of witchcraft by the Witchsmeller and convicted on completely ridiculous "evidence."
The Metallica song "The Shortest Straw" is about witch hunts and blacklisting.
The music video for the Stargate remix of the Depeche Mode song ''Personal Jesus' has some villagers "dunk" a suspected witch.
In the role-playing game Paranoia, the entire underground society the players inhabit is nothing but one gigantic witch-hunt for commie mutant traitors.
For added fun, the player characters are always mutant traitors. Being a commie is optional.
It gets worse: the society itself is communist, and everyone in it (not just the PCs) is a mutant. For added fun, the rules of the complex as they are means everyone is a traitor just for existing.
The back story to the Boston Sourcebook to Mage: the Awakening provides detailed and accurate information on the Salem Witch Trials (no burning the witch there) and notes that the genuine mages of Massachusetts held it to be a warning of how cautious they should be if they wanted power in the New World. At the time of the actual trials, the mages had little to do with the proceedings, since they were too busy summoning monsters to help them fight off cannibalmutants.
One of the complications for the returning Solars in Exalted is that the Immaculate Order has spent millennia painting them as demonic "Anathema" in their holy teachings. This label applies to Lunars and Abyssals as well, and seeing as a Deathlord sacked a major cultural center just a few years back, everyone's keeping their eyes open for possible Anathema. It really doesn't help that incautious spending on Essence leads to lighting up like a Christmas tree...
Happens a lot in Ravenloft, particularly in Tepest, where an Inquisition targets anyone whose actions might be influenced by the shadow fey, and in realms such as Paridon where the monsters impersonate humans.
Subverted, however, in more conventional Dungeons & Dragons settings. As noted in the Harry Potter example, real casters tend to be able to use their magic to avoid getting assaulted (Mass Charm Person, for example) or make killing them too costly to be worth it. Assuming the wizard in question doesn't simply vaporise your village for trying, there's a nasty spell called Contingency that can do anything from teleporting the wizard away the moment you set fire to the stake to causing a huge portal to open up and start spewing The Legions of Hell into your village upon his death to any combination thereof.
Except for Dark Sun; while they don't usually bother with the burning, the sentiment and its effects — root out and kill all arcane magic users — is the same. Justified because Magic is Evil in this setting, being powered by sucking the life out of the plants and earth around you.
In Shadowrun, Aztlan has it as bad as the real-life Soviet Union, complete with priests teaching children to report "subversive behavior" in their families.
Many Inquisitors in Warhammer 40000 do this as their standard M.O., complete with Kangaroo Courts to try the accused en masse and the burning of the convicted alive. (Literal charges of witchcraft in such cases are common, but not mandatory. Accusations of heresy, mutation, corruption, or alien influence may also be leveled.)
In Baldur's Gate the Bhaalspawn usually aren't trusted or loved, even compared with "normal" treatment of tieflings (it figures). The Witch Hunt against them is not entirely unjustified, except that those witch hunters you meet don't ask any questions, and if they do they don't care at all what you say. And then it all ends in a massive war, as the last survivors come together with their armies to decide who will be the one.
The Witcher: In the Crapsack World continent of The Witcher there were severall officially mandated pogroms against non-humans such as elves and dwarves. In addition, there is Abigail who is a witch living in a village in the Outskirts. Despite buying her herbs and potions, this doesn't stop the villagers from forming an angry mob under the local priest and trying to lynch her. The protagonist can either save her so she leaves the village for good or let her die.
Monster Girl Quest has a "Witch Hunting Village" and its officers going around accusing people into witchcraft then take them to the mayor's manor. Ironically, the mastermind is a mad witch and scientist herself.
In La Pucelle, the group finds themselves several years back in time, where the followers of their goddess are being hunted as witches.
Sentinel Prime touches off one of these in the third season of Transformers Animated, even making propaganda shorts warning that anyone could be a Decepticon. It's slightly justified, since the last Decepticon spy was the freaking Head of Autobot Intelligence.
There are a good number of examples of Truth in Television, and not just witches. It's worth noting that often the thing that turned an ordinary investigation into a full-fledged witch hunt was... politics!
The Fifties-era Red Scare, spearheaded by Senator Joseph McCarthy, ruined the lives of genuine political communists and the falsely accused alike. Today in America, "McCarthyism" is synonymous with political fearmongering.
Interestingly, this was such a Witch Hunt that the aforementioned play The Crucible was written in response to and as an allegory of McCarthyism.
The Spanish Inquisition, which sought to root out heresy. And witchcraft. And people falsely claiming to be Christian.
And because the Spanish Inquisition insisted that ordinary standards of evidence applied in witchcraft cases, they didn't have witch hunts like France or Germany did. The sole witch hunt was the Basque witch trials — and the Inquisition punished the friars involved for their involvement.
The Landlord Purges during the rise of Maoist China.
The fear that you could be reported—often falsely—for subversive behavior by anyone, including your fellow workers, and sent off to a work camp or killed was one of the keys to Stalin's power in the Soviet Union.
Even by your own children in some cases. Kids were encouraged by the Stalinist government to report subversive behaviour in the privacy of their own homes, adding another layer of fear. Several past totalitarian governments have used this.
The Fugitive Slave Act of the pre-Civil War period had Southern slavers be able to come into the North and reclaim slaves that had fled there. However, since there were plenty of free black people and not very many people cared about blacks that much, the slavers could just point a finger at a free black that had lived in the north all his life and say "That's him." It's no wonder that many Northern states passed laws greatly restricting the enforcement of the Fugitive Slave Act whenever and wherever they could — something that pissed off the South to no end. Many Southern states cited the North's collective refusal to enforce the Act in their declarations of secession.
A wave of witch panic went over Sweden in the years 1668-77 after a rumor started that witches were targeting children and abducting their souls in their sleep to offer them to the Devil. In one case, the Torsaaker trial, 71 people were beheaded and burned after a fanatical priest had forced local children to testify against them.
It used to be said that the Gestapo had a spy on every corner looking for anyone who might be a threat to the Reich. Actually, the civilians would use the Gestapo to settle old scores.
This was seen during the occupation of Paris. French citizens used the Gestapo to eliminate rivals. Some people were released with a warning after interrogation, others were sent to prison camps. 
Modern first-world example: the "Satanic Panic," which took place from the 1970's to the 1990's in the US and UK. Thanks to people like Mike Warnke publishing books like The Satan Seller (later discredited), people became convinced that massive numbers of Satanists were engaged in all sorts of nefarious activities, including but not limited to underground child pornography rings (using children left at daycares), sacrificing people, putting subliminal messages in everything to corrupt the youth, and trying to take over the world. People were convicted with the flimsiest of evidence, and many of them are still in prison today.
A modern one is the outgrowth of the Pædo Hunt obsession. Anyone even accused will be instantly convicted in public opinion and their life ruined forever, even if they are completely exonerated or never actually charged with anything. In a lot of America it's risky for a man to appear in public with his daughter, much less exchange words with a child not his own.
The West Memphis Three are a trio of high school boys who spent nearly two decades imprisoned after they were convicted of murdering three young boys in the town of West Memphis, Arkansas. But the thing is, there was never any evidence actually linking the boys to the murders. During the trial the prosecution used the facts that the boys were social outcasts who wore black and listened to "satanic" Heavy Metal music as evidence that they must have been the ones who committed the murders. The jury bought it and the three boys were sent to prison. During the two decades that followed the conviction was criticized by legal experts and several documentaries were made supporting the release of the West Memphis Three. Finally, in August of 2011 the West Memphis Three were released after entering plea deals with the state supreme court.
The tabloid press in Britain are particularly bad at cooking up things like this. Charlie Brooker commented on the irony of one of the major players, The Sun, throwing the accusation of witch-hunting at critics of the paper; the video can be seen here.