Frieza of Dragon Ball Z suffers such a fate; after being the Big Bad of the entire Namek arc and beating just about every opponent who comes his way, he is bested when Goku becomes a Super Saiyan. His pride is broken and he is turned into a pathetic wreck, with Goku inflicting all kinds of humiliating injuries upon him, such as battering him down on the head to create a ridiculous, bug-eyed expression and slapping him back and forth in the face. This culminates in him being sliced in halfby his own energy disc, and his humiliation is only made worse when he is forced to beg for Goku's sympathy.
It all starts when Goku detects Frieza's power level is woefully inadequate and falling fast, so he literally turns his back on Frieza; and it ends with Frieza floating through space, all alone, still alive but weak as a kitten, literally cut to pieces.
Before that, though, all those killed by Frieza and his minions are revived, including the Namekians and Porunga. Frieza is able to vocalize his wish, but it has to be done in the Namekian language. Dende fulfills Goku's request and everyone, including Porunga, is transported to Earth. What follows is Goku rubbing that last failure in and Frieza screaming so loud it shatters nearby rocks.
Frieza is further humbled when he returns, his missing limbs replaced by mechanical substitutes, and is easily bested by the newly introduced Future Badass Trunks, who turns out to be a Super Saiyan too. Every attack he tosses at the young Super Saiyan is easily deflected before Frieza finds himself once again sliced in two, this time from head to groin, then cut up even further before being blasted into ash. His father King Cold fares no better, getting blasted through the heart after thinking Trunks is nothing without his sword and then vaporized against a mountainside. Doubles as a Crowning Moment Of Awesome for Future Badass Trunks.
This scene was different in the manga though — Trunks pretty much kills him immediately while he was distracted, and never tried to deflect a powerful blast from Frieza, preferring instead to dodge it. Not quite as humiliating, but still hardly a fitting end for the former emperor of the galaxy.
Frieza continues to be humiliated even after death; every time he is met in the afterlife or resurrected, he is easily put in his place by the ever-growing power of the good guys. For instance, in one of the many (non-canon) DBZ movies, after being revived along with all other evil beings, he is defeated with one punch by Gohan.
To top it all off, Episode of Bardock reveals that Frieza's own actions during the genocide of the Saiyans results in Bardock being sent to the past — where it's revealed that he is the Legendary Super Saiyan. Meaning Frieza created the very legend that he destroyed the Saiyan race for, an act that would lead to his death.
While not as ultra direct as other congas, if you watch closely the scene of the Code GeassGrand Finale where some of Emperor Lelouch's more recent and direct opponents, as well as the kidnapped UFN representatives, are paraded off to be executed in public, with only Nunnally being assured to not die, you'll notice that Schneizel is being subjected to a far more humiliating treatment. He's got Clothing Damage (hell, his clothes are gone, and he's got your classic rags as his "prison uniform", compared to everyone else's relatively neat and clean straitjacket ensembles), appears to have been beaten up during his time in prison and is also chained to his post, which is much larger and prominently displayed than those of all the others being shown off in the parade...
A more straight example happens much earlier in the series, and not even to a major villain. When Margrave Jeremiah Gottwald comes out from under Lelouch's Geass control, he's been arrested for treason, has no memory of what he's done to earn it, is offered the equally humiliating choices of being forced to work on an orange farm (as an insult to the "nickname" Zero called him to falsely imply they were allies) or being demoted back to a beginner-level pilot rank, and at least one of his former subordinates is willing to kill him because he's become such an embarrassment. And then, while trying to prove himself worthy of the empire and his former rank, he ends up going up against Kallen in her brand shiny new badass mech, and pays dearly for it. What'd he do to earn all this? Got on Lelouch's bad side by being the one behind Suzaku's scapegoating for the murder of Prince Clovis. The Humiliation Conga ended up being effective for an entirely different reason, as a large mass of the fandom thought it was Disproportionate Retribution, and rocketed "Orange-kun" to the role of Ensemble Dark Horse, assuring his promotion to a major antagonist and later to a simply memorableHeel-Face Turn.
In the Knightmare of Nunnally manga, a smaller and more comedic conga is dealt to a puppy-kicking Ashford Alpha Bitch and her Girl Posse, when they throw Nunnally off her wheelchair. Nunners's best friend Alice (a girl with Super Speed powers derived from her being injected with C.C's cells stands up for her, steals the bullies's school skirts and leaves their panties exposed.
In Axis Powers Hetalia, America is forced to apologize to the other countries for the horrendous mess that was the Great Depression. The reactions are different per nation, but as a whole, this is what happens (Hungary, France and Switzerland are particularly NOT pleased). And as icing on the cake... Russia is very pleased since his economy actually grew.
Zig-Zagging Trope: On the one hand, America has done something pretty bad and all the other countries are mercilessly letting him have it and blaming him for it all. On the other hand, America's not shown as a villain, just paying for his typical but this time irrational exuberance, and the other countries aren't really punishing him because they're mostly too busy freaking out over their collapsing economies. This being Hetalia, the whole thing is Played For Edutainment. The previous strip in the series displayed America's overproduction and debt accumulation as the cause. This being Hetalia, the whole thing is a roundabout soap opera way of getting Lithuania to end his outsourcing holiday from Russia. This being Hetalia, the Politically Correct History prevents the depiction of Hoover's actual response which would be best represented by giving the rest of the world a slap in the face, is not mentioned. It's not Ripped from the Headlines, in case you were wondering.
This happens a lot to the Team Rocket trio from Pokémon, usually at the end of an episode. It seemed to be a lot more frequent during Kanto, though. This usually would involve them running away from something or someone (Jessie, James, and Meowth being chased by Beedrill became a running gag, though it does happen to the good guys as well). One notable example had them tied to a moving carousel by Ghost Pokémon, who considered it all in good fun to see them get dizzy from nonstop carousel rides.
A nonvillainous example happened to Misty over the course of the episode "Pokemon Fashion Flash", when she played a somewhat antagonistic role. SheandAsh got into a fight out the virtues of inner beauty VS outer beauty, with Misty on the side of outer beauty. Ash sarcastically dared her to take Psyduck down to the salon (being run by Team Rocket) in order to prove her point, and Misty sincerely agreed to it. But when she got there, Team Rocket assumed she wanted a makeover and so they gave her a ridiculous new outfit and hairstyle, and when Misty actually liked it, they added more by painting random marks on her face, making her appearalmost clown-like.Then once she found out it was Team Rocket, they took her hostage and tied her to a chair. And she was still tied to the chair during the climactic fight when Vulpix let out a huge Fire Spin, which completely torched her. To top it all off, Ash reacted to her silly makeover by LAUGHING HIS ASS OFF. So the episode ends with Misty having made an embarrassment of herself and Ash getting the last laugh after all. Sucks to be you, Misty.
Grings Kodai, the Big Bad of the Pokémon: Zoroark: Master of Illusions, gets an exceptionally well deserved one. He got tricked into thinking he's gotten the Time Ripple he wanted the entire movie, tricking him into Evil Gloating which is caught on tape. He then gets the device he needed to absorb the Time Ripple destroyed and is sent running for his life by Zoroark and the Legendary Beasts. The mortally wounded Zoroark uses her illusion powers to send him falling off a stadium balcony and getting knocked out. When he comes too, he's surrounded by pretty much the entire cast and forced to watch as afor mentioned Evil Gloatingis broadcasted across the city on the TV network HE created. To put the cherry on top, he's promptly arrested on the spot.
Most of the villains in One Piece suffer this. According to Oda, it's more meaningful to prove a man's "way" wrong than to kill them. So what do the Strawhats do to every main antagonist? They beat them to a bloody pulp, crush all their hopes and dreams and let the Marines take care of the rest.
This is also often subverted as many of these same villains (almost always the more comedic ones) appear again in the manga's cover arcs, where they stumble upon shockingly good fortune and end up better off than most of the other characters in the series. Wapol gets a Hot Wife and becomes a rich industrialist, Hatchi befriends a cute mermaid, Gedatsu owns his own hot spring resort, some of the Baroque Works members get a Karma Houdini, Jango and Fullbody become marines, and Eneru forms a new empire on the moon. (Strangely, Eneru is actually shown getting away at the end of his initial storyarc, which makes it feel a lot like he pulled a Karma Houdini)
Since reaching the moon was Eneru's goal all along, there's a case to be made that his storyline was actually a case where the bad guy wins.
Hatchi eventually comes back and makes a heel face turn, so perhaps these side stories are Oda's way of redeeming those characters.
Caribou, full-stop. He pretty much became a Butt Monkey the moment he met the Straw Hats, getting consistently curb-stomped, captured, sent to the marines, escapes, gets stuck in a storm, gets saved by an old lady, and then mistaken as a commander in a rebellion. The man can't catch a break.
Jail: I've been keeping myself healthy. This transparent prison is unexpectedly comfortable. Cinque: Uno and Tre are healthy as well. Jail: They haven't changed at all. Quattro has even gotten a bit fat.
Mahou Sensei Negima!: While he isn't really a villain (he's a Well-Intentioned Extremist at worst), Kurt Godel undergoes one of these after he tries to convince Negi to join him. Not only does Negi kick his ass, but each of Negi's True Companions successively uses their abilities to either attack Kurt, or screw him over in some fashion. It's topped off by Kurt's old ally Takamichi showing up and blasting him.
Takamichi: "What's the matter Kurt? These youngsters seem to be beating you senseless."
Love Hina: In the 10th volume of the manga, Keitaro's little sister Kanako submits all of the Hinata's tenants to one to punish them for their constant abuse and mistreatment of Keitaro. She actually succeeds in driving the girls out of the house completely.
Father suffers this fate near the end of Fullmetal Alchemist. First, he manages to get Truth, but after a fight, he loses the recent souls he had obtained to pull that feat off. Then, he tried to steal some souls and make more Philosopher Stones to make up for the loss, only for everyone else to confront him and deplete his original Philosophers Stone. Next, as he begins to lose control of God, he utterly loses it and, desperate for any souls, tries to take a pinned-down Edward, only for Alphonse to sacrifice himself and give Ed his arm back, enabling Edward to pull himself free and deliver a No-Holds-Barred Beatdown on Father's ass. In a last-ditch effort, he reabsorbs his son Greed to acquire his Philosopher's Stone, but Greed, who'd defected long ago, uses his carbon-based transformation abilities to turn Father into charcoal at the cost of his life, which allows Edward to punch clean through Father and lose every last soul he had remaining. With no Philosopher's Stone left to contain God, he immediately implodes. Finally, Truth meets up with him, gives him a Breaking Speech, twists Father's own words on him, and permanently seals Father on the far side of the Gate of Truth as he literally screams for mercy. On the plus side, while Brotherhood tries to humanize him somewhat during all of this, for the most part he had it all coming.
In Sakura Gari, Dr. Katsuragi gets a truly spectacular one as punishment for all his horrible deeds. The boy he whips, rapes and tortures out of jealousy? Masataka burns his face badly by throwing boiling tea on his face, ruining his Tall, Dark and Handsome looks. The man he loves, whom he forced to kill his abusive stepmother when they were kids and the "reason" why he rapes the aforementioned boy? Souma confronts him over the torture of the poor kid, then tricks him into drinking a tea laced with the drugs Katsuragi has used to slowly kill Souma's father (at request of Sakurako, the guy's scorned half-sister), and when the "good doctor" is laying on the floor, he deals him a brutal "The Reason You Suck" Speech and goes away. The wife that he beats and abuses to terrible degrees? Once they're alone, Asayo he sets him on fire and kills him.
In He's Dedicated to Roses, Mi-Mi gets a positively epic one. The girl she's bullied, used, outed, and pretty much been a bitch to the whole series? I-Da realizes that she can't just let others push her aside, undergoes a physical and mental transformation and announces that she's not going to take any of that crap anymore, and she'll beat up anybody who tries. The boyfriend she's been manipulating the whole time and got sent to juvenile hall? Hak-Yoon breaks out, tells everybody that Mi-Mi was the one responsible for his Attempted Rape of I-Da, burns M-Mi's forehead, and tells her he'll be looking for her once he's out of juvie. This leads to everyone the the class hating her and spitting on her, and I-Da not punching her because she feels it wouldn't be worth it. She goes home, ready to tell her parents everything and getting I-Da's parents sent to jail, just in time to see her father being arrested for shady business practices, realizing that her uncle has told the police everything about them, and that they've lost all their money. And the boy she fell in love with, the reason she pulled all this crap? Na-Ru has fallen in love with I-Da. Mi-Mi pretty much breaks after all this, and ends up being a shut-in in her uncle's house, not seeing or talking to anyone.
Kurata from Digimon Savers gets an EXTREMELY well deserved one. Marcus manages to get ShineGreymon to digivolve to Burst mode, after which Kurata's life goes on a major downwards spiral. His One-Winged Angel form is systematically torn apart around him and he's reduced to begging for his life. Marcus and ShineGreymon then proceed to defeat him with one punch. Not a super flashy Finishing Move, but one punch each. To rub salt in the wound, all his back up plan to destroy the Digital World fails completely and results in his own death. Sure, it made things worse, but all Kurata ever saw was his plan backfire and kill him. Couldn't have happened to a nicer guy.
In Hunter × Hunter, after using one of their friends to force them to throw their fights, Gon and Killua show a nasty trio of Heaven's Areana fighters no mercy. Killua scares Sadansho so badly he leaves town, and Gon flattens Ghido under a giant tile before breaking his prosthetic leg. Riehvelt gets it the worst though—Killua flings him from his wheelchair and catches him with his own electric whips, and Gon scares him into fainting by stealing his whips and nearly electrocuting him at full power.
Awaki's introduction in A Certain Magical Index. One episode after she's introduced as an antagonist, she's been injured and verbally humiliated by Kuroko, forced to flee from Touma and a very angryMisaka, contacts her associates only to hear them being taken down by a SWAT team, and then runs into Accelerator...
Ryoko and Ayeka suffer from one in episode seven of Tenchi Muyo!. Having decided to team up to take care of their "rivals" Mihoshi and Washu, Mihoshi by sending her back to the Galaxy Police and by boarding up the door to Washu's lab, they end up turning on each other, the only thing standing between them and Tenchi is a teleportation trap on his door. As they fight, a frightened Sasami defeats the trap by knocking, leaving the two even more confused as they hear Washu in his room, too. They try to join them, but are quickly tossed out into the lake. As they pull themselves out, they're treated to having Mihoshi crashland on the house.