In Ranma One Half during the Moxibustion Story Arc, Ranma was weakened and Happosai (the guy who weakened him) told every enemy that Ranma had, and they all ganged up on him to give him a beatdown. All but one ...
Even Naruto manages to pull this off, by way of Kabuto's Edo Tensei, resurrecting many foes that either Naruto faced himself, or are enemies of the collected Shinobi villages as a whole. Worse, some of the line-up included some friends and family to the heroes!
Not exactly, since they are all victims of Mind Control, and though some have more problem with whats happening than others, most would gladly rip Kabuto's head off for what he's done to them. However, its played straight in-universe with Kabuto again, allying with Tobi who has allied with Sasuke, and revealed himself as the leader of Akatsuki (though most of them are now dead). Akatsuki also qualifies, since it is an organization hose membership includes the most dangerous criminals in the ninja world, though from an audience perspective most of them are new characters.
The first part of the Super 17 saga of Dragonball GT, where the gates of HFIL break open, releasing an army of villains from both the original series and Z.
Naturally, absurdly common in comic books. There was even a short-lived Marvel series, Super-Villain Team-Up.
Super-Villain Team up was actually a Non-Indicative Name seeing as most of it was supposed to be one or two villains working together. It mostly came down to Doctor Doom and Namor, though the last couple of issues were about Red Skull and the Hate Monger.
Another one from DC was the shortlived Secret Society of Super-Villains, in which a collection of old school villains form a sort of anti-Justice League of America and fight the newly-arrived Darkseid and company. In one memorable scene, Gorilla Grodd has a punchout with a giant club wielding member of the New Gods, and defeats him with the aid of a classic wrestling ploy, the heelishmock surrender. The Society even had their own series.
Later expanded during and after Identity Crisis. Witnessing the JLA's much more proactive stance after the murder of Sue Dibny, most of the supervillains band together and form an international organization. This version lasted up until Flashpoint and the New 52.
The whole premise of the miniseries Wanted is that the villains don't fall to bickering and instead destroy all the heroes and take over the world. (It's only after the heroes are gone and they are the unequivocal masters of all the world that the infighting starts, mirroring some Real Life political coups by politically expedient alliances.)
Another Batman example. In an issue of a Golden Age Batman comic The Joker and Penguin teamed up and were so good with their combined resources that Batman was powerless to stop them. He won only after they had captured him and he turned them against each other by stroking their egos to the point that they got into a competition and then an argument over who was contributing more to their partnership.
One of the earliest examples has to be the Injustice Society of the World who first fought the Justice Society of America in All Star Comics #37 in 1947, when the concept of supervillains was still relatively new. They would return (in different incarnations) to plague the JSA over the decades.
Media adaptations of the X-Men have an annoying habit of grouping most X-Villains as members of the Brotherhood of (Evil) Mutants with Magneto as the leader, regardless of whether or not said villain ever had anything to do with the group in the comics (Sabretooth, Emma Frost, and the Juggernaut, who's not even a mutant), or if they'd ever play second fiddle to anyone (Mystique, who led her own version of the team).
DC's Injustice Gang pretty much embodies this trope. The antithesis to the Justice League, they're a group of villains who band together to destroy the JLA. The lineup changes with every appearance, since the Gang tends to disband (or all be thrown in jail) at the end of a given story. Its most successful incarnations have all been led by Lex Luthor, perhaps due to his Genre Savvy nature; in one story, he tells his fellow members "let's not fall victim to the cliche of the villains who can't get along." He's also perhaps the only major supervillain who has been able to successfully enforce harmony and cooperation among his gang, with no dissensions, betrayals, or serious infighting — no small feat when you've got The Joker on your team.
The Ur Example is the Monster Society Of Evil, who fought the original Captain Marvel from 1943 to 1945 in one long, continuous story. It was led by the new villain Mister Mind, but was composed mostly of villains that the good Captain had fought before. And the entire Axis Powers.
In fact the first example may be from Leading Comics #1 (winter 1941) where the Seven Soldiers Of Victory formed. Master Criminal the Hand, thinking he will die soon, organizes five other criminals to use five unused schemes of his, referring to them as the Hand's Five Fingers. They are stopped by various heroes leading to the formation of the Soldiers. Interestingly enough one member, the Dummy, was a member of the first Monster Society.
In Ghost Riders: Heaven's on Fire, a Legion of Doom has been assembled to kill the Ghost Riders, consisting of Blackout (murderous vampire), the Deacon (musclebound religious zealot with sacred knives), the All-New Orb (Legacy Character to the original Ghost Rider archvillain), Big Wheel (baddie-for-hire who pilots a large metal wheel), Madcap (indestructible lunatic with contagious insanity), Vengeance (ex-cop turned Ghost Rider simulacrum), Trull the Inhuman (alien-possessed steamshovel), and Scarecrow (No, not that one, but rather a maniac with a pitchfork who commands crows).
The Masters of Evil are the most successful, with one incarnation taking over the Avengers' base (and beating the living crap out of Hercules and Jarvis). Much of this incarnation later went on to form the Thunderbolts. (Hercules, amongst others, was not happy to find out about this...)
And the Legion of the Unliving, which is made of characters currently dead, and in one incarnation was mostly made up of dead Avengers.
The Sinister Six has even become the Sinister Twelve.
A particularly enjoyable miniseries example came from Marvel a few years ago: M.O.D.O.K.'s 11. MODOK hires a group of supervillains to help him steal a MacGuffin. 3/4 of the team ends up being traitors, moles and sellouts. In the end, it was all just a ridiculously circuitous plot to get revenge on his ex-girlfriend.
The Flash has The Rogues, who started out as a Villain Team-Up in The Silver Age of Comic Books, but after discovering how well they worked together decided to keep working together. These days it's rare to see one of the Rogues commit a crime without some of the others around.
Fall of The Hulks gave us the Inteligencia, a group of Marvel's smartest villains. Unlike most examples, they've managed to not fall to bickering and work towards a common goal.
The Superman Revenge Squad, mostly made up of relatively minor or recently created Superman villains, was formed by behind-the-scenes bad guy Morgan Edge to fight Superman. The group ultimately failed due to a lack of cohesion.
An early Superman story had the Terrible Trio, made up of Lex Luthor, the Toyman, and the Prankster.
In Top 10, it's established that what would be supervillain teams anywhere else are essentially street gangs in Neopolis, where everybody is super. There's an ongoing turf war between the Fabulous Five and the League of Evil.
But there was also a Dark Avengers, with villains impersonating heroes.
Norman tries again when he busts out of jail following Fear Itself, this time allying his H.A.M.M.E.R. organization with A.I.M., Hydra, and the Hand, and once again uniting multiple villains (independent of those groups) into a new group of Dark Avengers. It doesn't work out for him any better this time.
Image's Guarding the Globe series introduced us to the Order, a select group of minor recurring Invincible villains, including the Face, Master Liu and his bodyguard, Octoboss, Multi-Paul, Machine Head, Isotope, and Titan — in addition to new guys like the group's leader Set, his woman Embrace, and international enforcers like Red Eye, Insomniac, Slaying Mantis, the Walking Dread...and War Woman.
Often times in Pooh's Adventures, there's a legion of assorted villains that are after Pooh, and there are times in the Adventures where the good chunk of them are featured as the main villains that team up with the villain of the film.
The 1966 live-action Batman: The Movie, featuring the Joker, the Penguin, the Riddler, and Catwoman ("United Underworld") in a cheesy penguin-shaped submarine. They even went through the trouble of making a logo.
The Joel Schumacher-directed Batman movies also have this as all the villains within the movie unite to kill Batman. Riddler joins and eventually leads Two-Face's gang in Batman Forever and Mr. Freeze allies with Poison Ivy and Bane in Batman & Robin. More or less subverted in Batman Returns where Penguin's two allies have no idea they're both affiliated with Penguin (at least on a criminal level) and none of them can get past the second act without completely and violently falling apart.
The final episode of Team Knight Rider, aptly titled "Legion of Doom", featured all the villains from the series teaming up under the command of the series' Big Bad.
Doctor Who has toyed with doing this on several occasions, but it never quite works out. In "The Five Doctors", many of the Doctor's worst foes are brought together to finish him off - but they are merely pawns of The Man Behind the Curtain, and apart from the Master and the Cybermen don't even interact. "The Daleks' Master Plan" is nearly an ideal example of the trope - a colourful array of supervillains is brought together by the Daleks; it includes a dominant, disruptive personality (Yellow Peril and Diabolical Mastermind Mavic Chen), and the heroes exploit the infighting. Just one problem - the Doctor's never met any of these bad guys before.
The new series episode "Doomsday" bring the Daleks and Cybermen together, however the Daleks, being the Daleks, respond to the Cybermen's offer of an alliance with summary extermination.
Subverted to hell and back in "The Pandorica Opens", in which a couple dozen races show up, apparently to squabble over whatever is imprisoned in the eponymous device, only to imprison the Doctor in an effort to save the universe. Seen on screen are the Daleks, the Cybermen, the Sontarans, the Silurians, the Autons, and the Judoon, and many more get name checks or cameos in crowd shots.
Kamen Rider Decade introduces a particularly large version in the form of Great Shocker, which is an alliance of every single evil organization from Kamen Rider's 30-plus-year history united under a single banner and dedicated to conquering the multiverse and destroying all the Kamen Riders. And their leader is Tsukasa Kadoya, AKA Kamen Rider Decade, one of —- if not —- the most powerful Rider ever. In Final Chapter, following Great Shocker's downfall in All Riders vs. Great Shocker, Doctor Shinigami and Narutaki (who reveals himself as Colonel Zol) gather The Remnant as Super Shocker, hoping to take advantage of the fact that Tsukasa's rampage as Destroyer of Worlds has eliminated all the Kamen Riders. Unfortunately for them, all the Kamen Riders are later brought Back from the Deadbecause Decade destroyed them (it's a complicated story). In Kamen Rider X Super Sentai Super Hero Taisen, Great Shocker has been rebuilt with its leader back into the seat and Doctor G as his Dragon, for a new purpose: the systemic annihilation of all the Super Sentai teams, simply because the Zangyack Empire decided to step on the Kamen Rider multiverse's toes —- see the Kaizoku Sentai Gokaiger section below for their side of the story.
In a smaller scale, the final episode sees Apollo Geist reviving some of the monsters that Tsukasa and company dealt with while travelling through the AR worlds.
The On the Next preview for episode 25 of Kamen Rider Fourze teased at this, where three previous Zodiarts that Fourze had already defeated seemed to have regained their powers, and are working together to sabotage the school prom. However, it turns out that this was just the work of a Zodiarts whose power is to create copies of previous Zodiarts.
In the Movie Warcrossover with Kamen Rider OOO, Foundation X uses the research its agents gathered to build an army consisting of various monsters as well as mooks from the three series involved (Fourze, OOO and W), alongside monsters of the Big Bad's own design, called "Mutamids". They are not essentially the same monsters from their original series, but it's an excuse to reuse monster suits.
The final episodes of Kamen Rider Den-O features the Big Bad amassing an enormous army of the series' Monster of the Week in order to outnumber the heroes (two Riders and 5/6 Imagin) and accomplish his plans. This army would later be resurrected in the third movie, Final Countdown, under the movie's Big Bad.
In Kamen Rider X Super Sentai Superhero Taisen, Zangyack has been expanded into "Great Zangyack" by the hands of their new emperor, who appears to be a Face Heel Turned Captain Marvelous, AKA Gokai Red, who launches an invasion of the Kamen Rider multiverse to claim the Riders' Grand Powers; its membership includes a number of high-level villains from all over the Super Sentai franchise like Doukoku and Bio Hunter Silva.
Angel Season 5 makes use of this by taking several minor characters that appeared throughout the season and putting them in a group called the Circle of the Black Thorn, which the heroes spend the last episode combating. Sort of an inversion—rather being a group of random villains that teamed up, they had already been working together, though Angel and his friends didn't find out until later.
In the first season of Series/Blackadder, Prince Edmund gathers the six most evil men in England to help him take over the kingdom. However since he doesn't really belong among their number, much less leading them, they quickly betray him for a more fitting leader.
Sue's self-described Leg - uh, League of Doom in Glee, if you replace "supervillain" with "returning character with a grudge against the local show choir". She even gives them code-names, dubbing herself General Zod.
Chester, a now-classic William Billings song from the Revolutionary War, devotes a verse to what sure sounds like the British Legion of Doom circa the 18th Century.
Howe and Burgoyne and Clinton, too
With Prescott and Cornwallis joined,
Together plot our overthrow
In one infernal league combined.
Legendary Professional Wrestling stable The Four Horsemen started out as a Legion of Doom-esque gathering of heels. Rated RKO was the teaming of two of DeGeneration X's biggest rivals, and DeGeneration X itself was originally formed to fight against The Hart Foundation. There is also a tag-team called the Legion of Doom, but they're not an example of this trope. And we can't let the Pro Wrestling entry go by without a mention of the nWo, can we?
By the time they entered the WWF the LOD might have been a tag team but in GCW they were actually an example of this trope and included such other future legends as Jake the Snake, The Spoiler, Matt Borne (AKA the first Doink the Clown), King Kong Bundy, Arn Anderson, and for perhaps the only time both of the Sheiks, Iron and Original. The two remaining members were made into a tag team and were supposed to be called The Road Warriors hence why they are introduced as "Road Warrior Hawk" and "Road Warrior Animal". The two names have been used interchangeably since then.
During Uncensored '96, two of the groups above united to create an even bigger Legion of Doom when the Four Horsemen and the Dungeon of Doom joined forces to become the Alliance to End Hulkamania along with two random wrestlers The Ultimate Solution (the late Robert "Jeep" Swenson, aka "Bane" from Batman & Robin) and Z-Gangsta (Tom Lister, Jr., who played Zeus in Hulk Hogan's 1989 film No Holds Barred). They fought Hogan and Randy Savage in the "Doomsday Cage Match", a triple-decker cage. However, at the apex of his Invincible Hero status, Hogan was still too much for the eight members of the Alliance and he and Savage soundly beat them.
There's a sort of example done apparently just for the sake of simplicity in the games Hero Quest and Space Crusade, roughly based on Warhammer and Warhammer 40,000, respectively. In both games the bad guys are ostensibly "Chaos", but in fact their units are a combination of Orc, Undead and Chaos / Ork, Tyranid, Chaos Android and Chaos Space Marines characters, all united under the control of the same player to destroy humanity.
Villains And Vigilantes has an introductory adventure, "Crisis at Crusader Citadel," which has an NPC hero team, the Crusaders, and the Crushers, a villain team made up of their archenemies. Although it only points out who a few of the feuds are between.
The stage play Doctor Who: The Ultimate Adventure uses this trope, combining Daleks and Cybermen for the first time (outside of "The Five Doctors," when the Dalek basically cameos), although the two sides (not surprisingly) end up feuding.
Technically, the earlier stage play Doctor Who & the Seven Keys to Doomsday also uses the trope, combining Daleks with Clawrentulars, but since the latter have not appeared before or sense, they amount more to henchmen and one-off baddies.
In Kingdom Hearts I, various Disney Villains banded together under the command of Maleficent from Sleeping Beauty. As with most of the (relatively rare) video game cases, the villains didn't turn on each other; instead, the heroes picked them off one by one. Though Maleficent was the leader and the last required to fight, Hades was actually the most powerful (being a god and all) and thus, fighting him was left entirely optional until Kingdom Hearts II.
The premise of Nicktoons Unite is that Jimmy Neutron's nemesis Professor Calamitous steals his plans for a dimensional portal to form an "Evil Syndicate" consisting of him, Vlad Plasmius, Plankton, and Mr. Crocker. Naturally, Jimmy pulls the reverse and just like the first Kingdom Hearts mentioned above, you pick them off one by one 'till the pseudo-Boss Rush climax. And despite all four members being captured at the end, the syndicate reappeared three games later in Globs of Doom but with a different lineup of four (Plankton being the only "veteran" out of them) and only serving for a Enemy Mine situation (Well, until the Snap Back). Nevertheless, both incarnations never got to infighting at all.
Dissidia: Final Fantasy has a Legion made up of the main bosses from the first 10 Final Fantasy games, headed by the god Chaos, and opposed by the heroes of the same. They're not exactly the most cooperative of groups: They seem to have split between the Destroyers, Schemers, Defectors, and those who are just plain following their own agenda. But really, that's what you get when you assemble people that are this unhinged and expect them to get along.
In Super Smash Bros. Brawl's Subspace Emissary story mode, a group of villains, including playable characters Bowser, Ganondorf, and Wario, and NPCs Petey Piranha, Porky, and Ridley join under Master Hand, who is secretly being controlled by Tabuu, to make the Subspace Army. Bowser, Ganondorf, and Wario all end up eventually betraying the army, joining the heroes once they realize they were just Tabuu's pawns. However, Ganondorf planned on overthrowing Master Hand and becoming the army's leader long before he learned of Tabuu.
Marvel Ultimate Alliance features a virtual army of supervillains forming a new Masters of Evil, as well as several cutscenes in which Doctor Doom plot his evil schemes along with his flunkies, er, allies, Loki, the Enchantress, Baron Mordo, and Ultron (one assumes Ultron was frequently pinched for forgetting to wear green).
The Black Cloak Society of King's Quest was designed as a passing mention in an incriminating letter for the sixth game. However, the way the letter's worded implies that at least three of the series' Big Bads were part of the society...and possibly all of them were either members or allied with them. The Fan Remake of the second game and the Fan Sequel have run with the "possibly all of them" theory.
In Viewtiful Joe, the bad guys are an evil organization of all of Captain Blue's old villains, who have taken over since his defeat and living the life. Turns out that it was Captain Blue himself who was their boss!
And in the sequel, another evil organization takes their place, who's roster includes Alastor from the first game and Fire Leo's brother, Frost Tiger, and is run by Joe's father, who's been corrupted by the Black Film and the Black V-Watch.
Marvel Avengers Alliance has most of Marvel's supervillains from Hydra to the Brotherhood of Mutants uniting and forming the Syndicate, their goal is to harness Iso-8 and take over the world.
The Axis of...Something in Shortpacked!, comprising the guy who insists disagreeing with him makes Ethan "arrogant", Walter Mondale (seeking revenge on Reagan) and Faz. Their leader is a character who was fired from the store in her first appearance and has been plotting revenge ever since (ironically, this was what convinced Robin that nothing significant ever happened at Shortpacked, since none of the important characters were fired. Guess she really shouldn't have pulled that drama tag).
The Crossoverlord assembled one of these by gathering enemies of each story's main characters — at least one for each hero, two in the case of Dasien, but none for The Green Avenger (maybe because her only enemy at the point was a walking alarm clock, or because she was brainwashed).
In The Order of the Stick, the Inter-Fiend Cooperation Commission is an alliance of the three fiendish races (demons, devils and daemons), who have traditionally competed against each other. Different from most of the above cases because its three leaders were never actually seen prior to the team-up.
However, one recurring secondary villain (Sabine) was revealed to be working for them covertly behind her boss/boyfriend's back, and another minor villain introduced during the same arc (Qarr) was recruited to serve them during their initial appearance..
The Warriors of Darkness in Eight Bit Theater, four villains assembled to be the opposite number to the Warriors Of Light.
The Warriors Of Light probably count too, having a kill streak spanning several continents worth of genocide and the KT event.
Team Kimba of the Whateley Universe is viewing Elite League as this. They have fought the Young Turks twice before, and a lot of the Alphas, and Gold Stallion's gang. Now they're seeing a team made up some of the best of those groups.
Batfink had in episode 96 out of 100 a conglomeration of villains brought together by Tough Macduff, Batfink's 'Oldest Foe', though this is his first appearance. They consist of Manhole Manny, Big Ears Ernie, Gluey Louie, Stupidman, Skinny Minnie, Whip Van Winkle, Old King Cruel, Cinderobber, Swami Salami, Party Marty, Beanstalk Jack, Queenie Bee, Sporty Morty, Roz The Schnozz, and, to add insult to injury, Hugo A Go Go, the mad scientist. They tell Batfink to be branded a coward and leave town on a train. However Batfink caches them all in a fishnet.
Another episode has one brief part near the ending where to get revenge on Buttercup (for repeatedly attacking them all with no provocation to get teeth in a typical tooth fairy story) a bunch of villains get together and beat her down.
Kim Possible, "A Sitch In Time" (sic), wherein the biggest villains join up in a Time Travel scheme, and get double-crossed by Drakken's sidekick Shego.
Justice League featured this thrice: the two versions of the Injustice Gang in the episodes "Fury" and "Injustice For All", and the Secret Society in the episode "Secret Society" (naturally, after the above comic). The sequel series, Justice League Unlimited, had another such group, albeit much larger and better organized, the focus of its third-season arc; this group was unnamed, but was variously called the Legion of Doom and the Secret Society by fans. (Lex does refer to it as a "society" at one point.) The entire third season was basically a homage to the aforementioned Superfriends, complete with Darkseid showing up as the True Final Boss to replace them.
The creators have admitted that they considered the massive villain group in JLU to be the Legion of Doom (complete with "Darth Vader head base in a swamp"), and generally referred to the group as such when discussing it, but had been explicitly told by DC that they could NOT use the Legion of Doom term. This is why the group is never actually named in the show, and why Luthor's allusion to the group implies it's related to the prior Secret Society. Note that Grodd corrects Luthor and implies the group ISN'T just a larger Secret Society - but then fails to provide an alternate term.
Interestingly, they were referred to as The Legion of Doom on the JLU Season 2 DVD box.
Justice League also featured the Superman Revenge Squad, though they were not named as such.
The original Secret Society was something of an inversion of this trope. Grodd uses his mental powers to make the heroes more irritable, causing them to give vent to grievances that they normally kept bottled up. This causes the dissolution of the League, much the same way that a normal Legion Of Doom will fall apart. Grodd even lampshades the common fate of Legions Of Doom, and seeks to avert it using trust-building exercises and training.
The episode with the Justice Guild has the Injustice Guild, based on the Injustice Society.
As the name would imply, the Legion of Doom are featured as the main villains of Justice League: Doom.
Aqua Teen Hunger Force subverts this trope in the episode "The Last One", in which the Mooninites gather all the..."villains"...that have appeared in the series to form a Legion of Doom. After the group's decimated because of its members' stupidity and annoyance with each other, the survivors dub themselves "Sunday Monday Tuesday Wednesday Thursday Friday Saturday" and launch an assault on the ATHF's home — which, of course, goes nowhere.
The enemies of Darkwing Duck join forces to become the Fearsome Five, forcing Darkwing to create his own team, the Justice Ducks in the episode "Just Us Justice Ducks".
Used (And made fun of) in the Third Season Premiere Show of Duck Dodgers, where nearly every minor one-or-two-episode villain was brought together (Sometimes from the dead) to form the Legion of Duck Doom, as the primary antagonists, Mars, were currently at peace with Earth. (Though by the end of the episode, the Legion is defeated, and war breaks out again.)
There was even a Captain Ersatz of the Black Manta called the Black Eel (who really shouldn't of been there, as he had no quarrel with Dodgers).
The Council of Doom was the collective name of Space Ghost's sworn enemies: Brak, Zorak, Moltar, Black Widow, Creature King and Metallus.
It should be noted that the Council of Doom appeared over a decade before the Trope Namer.
In an episode of Courage the Cowardly Dog, Eustace organizes a team of former villains into a group in order to kill Courage, ranging from recurring (arguably) nemesis Katz to the giant foot fungus, apparently ignoring/forgetting that they've endangered his own life before. They then proceed to brutalize Courage in a game of Dodgeball before he buries them in an earthquake caused by his own ability to scream.
Transformers Animated has a slew of B-list villains, and in one episode they come together to form the Society of Ultimate Villainy, to try and not get beaten up for a change. Hilarity ensues. Even all together, they still get upstaged by a Decepticon.
Earthworm Jim faced a team composed of all the major villains from his cartoon series. The stake? An egg-beater! No, a normal egg-beater, like the kind you have in your kitchen. Don't question the humor!
An episode of Spongebob Squarepants features a coalition of The Dirty Bubble, Manray, and the recently-turned-evil Barnacle Boy ("That's Barnacle Man!), calling themselves "Every Villain Is Lemons" (E.V.I.L.). This being SpongeBob, they accomplish about as much as you'd expect.
Erm, but E.V.I.L. WINS in that episode. It's only the fact that Barnacle Boy/Man's demands are so modest that scuppers his allies' plans. "C'mon - WORLD DOMINATION!..."
But during the Everybody Laughs Ending, Man-Ray and the Dirty Bubble are revealed to be in jail. Sure, they might have won the physical fight against the heroes, but they still make no progress at all due to Barnacle "Man"'s meager demands.
Apex tried to make one in an episode of Sushi Pack (partly as The Plan), but due to the villains' lack of respect for each other, they barely got past the planning stages.
The Crimson Chin webisodes had "The Body of Evil".
In "Escape from Unwish Island", Timmy's vengeful no-longer-imaginary friend Gary assembles all of Timmy's 'most violent Timmy hating wishes' that Timmy had unwished (as well as a Sphinx that he didn't) to get payback on Timmy for 'abandoning' them. Thought they manage to win, Timmy works things out with them.
In "The Big Superhero Wish", Timmy makes the world like a comicbook, resulting in superheroes and villains. Taking advantage, the Nega Chin (the Crimson Chin's alternate reality evil self) forms a supervillain group out of the now superpowered Crocker, Vicky, and Francis, complete with a swamp based 'hall of evil'. While they manage to win and take over the world, they're ultimately defeated by Timmy and his powerless friends.
In Johnny Test, five of Johnny's past foes form the 'Johnny Stopping Evil Force Five' to take their revenge, complete with a 'swam lair'. Similar to their counterparts, they actually manage to hold together and reappear in several future episodes.
The Batman's done this at least twice: "Team Penguin" in the episode of the same name, and briefly in "The Batman/Superman Story, Part One". However, the latter is sort of subverted as it may be members of Bats's Rogues Gallery teaming up, but they were assembled to fight against Superman.
The Spider-Man (1967) animated series in one of the last episodes had three foes who had each appeared in two episodes, Electro, Green Goblin and the Vulture, being broken out of jail by exclusive-show villain who had already appeared, the Invisible Scientist Dr Noah Boddy. Spider-Man tricks them into fighting each other with a crash course in ventriloquism, then webs up Noah Boddy.
The 1990s Spider-Man animated series had the Sinister Six, though they were called the Insidious Six because of worries over using sinister on a kids show.
The 200th episode did this with Tom Cruise gathering celebrities that the show had made fun of, like Rob Reiner, Paris Hilton, George Lucas, Mel Gibson, etc. Trey Parker and Matt Stone even used the term "Legion Of Doom" when referring to this episode in an interview.
The very first time it happened in was in "Operation: M.O.V.I.E.", where Numbah Four tries to get into an R-rated movie, only to find that it's a very large gathering of the KND's Rogues Gallery, summoned by Mr. Boss.
A larger scale version happened in Operation: Z.E.R.O., where Father (and later Grandfather) uses every possible villain against the KND. It is even stated early on that the KND had never faced such a coordinated attack from their adult enemies before.
Minor example in "Operation: F.L.U.S.H.", where Mr. Boss (again) gathers a Five-Bad Band version of this, only for the Toiletnator, rejected from the group, to defeat them on his own, since he mistook them for the KND!
Another Five-Bad Band would be in "Operation: M.I.S.S.I.O.N.", only it's Numbuh Four who assembles four incarcerated villains...for a bowling match against his father.
Mirroring the comics it is based off of, The Avengers: Earth's Mightiest Heroes has the Enchantress gathering up various villains to form the Masters of Evil. And then she gives the reigns to Baron Zemo, for some reason.
"Zemo is but a toy. To be discarded when I tire of him."
Avengers Assemble features the above-mentioned Cabal from Dark Reign as the principle antagonists. Red Skull even explicitly states that he formed them as the villainous equivalent of the Avengers.
The Knights of Vengeance from W.I.T.C.H. could be seen as one, as it was a gathering of various Phobos cronies united by Nerissa.
The Injustice League and the Light from Young Justice. As an Easter Egg, the Injustice League's hideout is an homage to the Legion of Doom's lair from Superfriends.
Family Guy mentions the Legion of Doom by name, when during Lois's bid for mayor, she claims they've teamed up with Hitler to assassinate Jesus. Cut to the Legion, with Solomon Grundy admitting he "dropped the ball on this one."
Xiaolin Showdown's series finale, after getting its own plotline resolved, ended with our heroes facing a Legion composed of every single villain in the series.
The second season finale featured a smaller Legion formed by Jack Spicer. They had the heroes on the ropes for a while until Chase Young stepped in and went Eviler than Thou on them.
The Mask episode "Convention of Evil", where most of the Rogues Gallery attend a therapy session hosted by recurring character, psychologist Dr. Neumann. The climax of the episode reveals that The Mask is in the meeting, disguised as Neumann himself.
The Legion of Doom is featured in the episode "Triumverate of Terror!" The episode sees The Joker joining forces with Lex Luthor and the Cheetah to finally do away with Batman, Superman, and Wonder Woman once and for all.
The Cold Opening of that episode was a baseball game between the Justice League International and the Legion of Doom, with Joker, Luthor and Cheetah united with Weather Wizard, Clock King, Chronos, Felix Faust and Amazo.
"Night of the Batmen!" features an instance of a number of Batman's foes teaming up to take advantage of Gotham City while the Dark Knight is in traction.
The Spectacular Spider-Man uses the Sinister Six twice. The first time has Docter Octopus, Electro, Sandman, Rhino, Shocker, and Vulture. The second team up trades Doc Ock and Shocker for Mysterio and Kraven.
In My Life as a Teenage Robot episode 'Legion of Evil', the titular Legion is made up of Jenny's enemies. The twist is that its membership consists of her least-threatening enemies; The Hammer Bros, Lancer, Mudslinger, and led by Dr. Wakeman's deranged lab rat Vladimir. Jenny was not impressed.
Jenny: Your name is Mr. Scruffles, your Legion is a bunch of B-list villains, and your secret lair smells like fish.
In Regular Show the episode "Exit 9B" has a Legion of Doom formed from the bad guys that got killed over the past 3 seasons all led by the son of Garrett Bobby Ferguson