D.Gray-Man: The Clan of Noah are a group of nigh-immortal Omnicidal Maniacs who want to destroy the world and who use weapons powered by suffering human souls, but they truly love each other. Even the Millennium Earl, who is technically their master (they never address him as anything other than the equivalent of "Lord Millennium"), is part of the family, acting more as a loving and much-loved family patriarch — he even gladly puts on a Martial Arts Headband and helps the youngest-looking Noah, Road, by doing her homework for her. Road is also very fond of The Hero, Allen Walker, and would love for him to be able to join their family. She gets her wish, much to Allen's dismay, when it turns out he is the host for the 14th Noah.
Star Blazers/Space Battleship Yamato has an interesting subversion in the second season: Zordar and Desslok understand each other, so Comet Empire generals and Invidia are just irritable when both Zordar and Desslok are around. When they're behind Zordar's back, they start acting like playground bullies and finally throw Desslok in prison.
The Secret Six (or at least Catman) believe Evil Is One Big Happy Family in the DC Universe... and it's a family they don't want any part of. They see themselves (or at least Catman does) as occupying a middle ground, rejecting both the Secret Society of Super-Villains and the Justice League of America. Of course, they're hardly the only villains to be on the outs with the Society....
The Society itself began to fall apart shortly after Infinite Crisis and was effectively dead by the end of Final Crisis. Having your entire organization get possessed by Darkseid tends to put a crimp in your membership renewals.
Supreme has Daxia, a realm composed of hundreds of versions of his nemesis, Darius Dax. They have the occasional bout of bloodshed among one another, but mostly get along pretty well.
Played with in the Marvel Comics event Acts Of Vengeance. Loki gathers together some of the great supervillains of the world (and the Wizard) as part of his plot to destroy the Avengers, and expects them to play nice together. Unfortunately, this involves putting the Red Skull (epic Nazi) in the same room as the Mandarin (Chinese), Doctor Doom (Gypsy), and Magneto (Jewish). They start out insulting each other, and eventually Magneto seals the Skull in a windowless room with no particular plans to let him out.
Turns out that Loki both expected and intended this.
The Marvel Universe in general mostly averts this trope, as most of the major villains have mutually exclusive goals or simply don't play well with others, which is why villain teams like the Sinister Six and the Masters of Evil tend to have such high turnover rates. This was probably best demonstrated during the Secret Wars crossover event, when the Beyonder placed all of the villains together in one team and apparently expected them all to get along. What actually happened? Ultron immediately tried to kill everyone, Doctor Doom and Galactus left to do their own thing, and the others started squabbling over who would lead the group.
Averted in Forever Evil. While the villains of DC Comics want to take over, not everyone has the same goals. This causes confrontations; especially when the Crime Syndicate appears.
In Charmed Episode 9 season 4 A Muse to My Ears, two warlocks harass a shape-shifting demon.
Demon: Back off; we are on the same side.
Of course, they kill him anyway to take his power, but that is beside the point.
Star Trek: Deep Space Nine: Weyoun quotes it almost word for word in "The changing face of evil". Subverted since Damar starts to organize his betrayal in this very episode.
In Merlin during and after season three almost every villain that appears either works with or for Morgana. She also works with the bad guys several times before season three.
Films — Live-Action
In Star Trek VI: The Undiscovered Country, it turns out that elements from both the Klingon government and Starfleet are working together to destroy the peace process between their nations. They are, in essence, working together so they can get back to kicking the crap out of each other.
In The Cabin in the Woods once unleashed monsters of all sorts attack only the humans, even though several of them want to do different, often mutually exclusive things to them and there's a limited supply available. Indeed at one point a zombie throws a man off a balcony into the jaws of the giant snake beneath instead of biting him itself.
Slacktivist has argued that this is part of the worldview of the Left Behind series, although perhaps "evil" should be substituted with "everyone who is not part of the Rapture-able Christians". For example, the world's Hindus, Muslims and Catholics show little opposition to an enforced worldwide pantheistic/polytheitic religion, since that's the sort of thing the authors believe liberals would like, and if you're not a member if the correct Christian sect, you're some kind of liberal. The Insane Troll Logic behind this being is that every false religion were originally created and are maintained by the Devil to serve his purposes, so if the Devil decides to merge them all together into a global religion, all their adherents shouldn't have any problem with it.
Although there are plenty of examples in the book of factions against the Global Community who aren't Christians: The Militia, some Muslims, Israelis. There are definitely some tokens who show up and act out their stereotypes. But the rest of the world just drops everything and joins the EBOWF (or whatever) because the authors couldn't imagine that anyone who wasn't of the same faith as the authors would value their own belief system as much as the authors value theirs.
In Paradise Lost, Milton suggests that this is actually something the devils do better than humans, even though humans have the potential for good:
O shame to men! Devil with devil damned Firm concord holds, men only disagree Of creatures rational, though under hope Of heavenly grace: and God proclaiming peace, Yet live in hatred, enmity, and strife Among themselves, and levy cruel wars, Wasting the earth, each other to destroy...
Old-time (pre 1990ish) Professional Wrestling was like this. All the faces liked each other and worked for the common good, and all the heels at least tolerated each other and worked for the common... bad(?). Until someone inevitably did a Face-Heel Turn or Heel-Face Turn, of course; then all the heels liked the former face or the faces liked the former heel, as the case may be.
This was one of the first tropes to be phased out as part of WWF's more realistic, Darker and Edgier reinvention in the late 90s, mainly because it really didn't make sense for, say, a Wild Samoan to be allied with an evil tax accountant against cowboys teamed with bikers.
For whatever reason, a group of heels is infinitely more likely to form a Power Stable like the Corporation, the New World Order, Evolution, the Main Event Mafia, or The Nexus than a group of faces. Usually, a heel stable is (at their start) is a well-oiled machine while the faces they fight just barely get along. Members of the stable will often go to extreme lengths to help their mates (such as run-ins) in comparison to their rivals. While a heel stable never lasts, a powerful one may take several months or even a couple years before they truly crack apart.
The main reason probably being that, in (ostensibly) a sport based primarily around one-on-one competitions, assistance from allies is often cheating; naturally, this bothers heels less than (traditional) faces.
The Dungeon Master's Guide for Third Edition Dungeons & Dragons cautions against this kind of thing in its advice about villains in chapter 5, under "Handling NPCs". "Monolithic evil is unrealistic," because "the goals of one selfish, destructive creature by definition conflict with the goals of other selfish, destructive creatures."
The 2nd edition Player's Handbook also calls out this type of thinking, stating that "a group of players playing a harmonious evil party are simply not playing their alignments correctly".
In In Nomine, if you analyze the networks of friendships and enmities among the powers of Heaven and Hell, you find that Hell has larger, more stable blocs, than Heaven does. (On the other hand, rival demons try to kill each other, while rival angels are usually just rude and obstructive.) Which effectively implies that "evil is a happy family" because who doesn't play along doesn't survive.
The Warhammer and Warhammer 40,000-based board games Hero Quest and Space Crusade. In both cases, the semi-GM-like evil-side-player plays "Chaos", but commands a combination of orcs and goblins, undead and Chaos forces in the first; and Orks, Necrons, Tyranidsnote Admittedly, this means genestealers that appear semi-randomly rather than being placed along with the other "Chaos" troops at will, so even though they are controlled by the same player, there's some implication they're working on their own. and Chaos Space Marines in the second. In the original wargames, these are all mutually hostile factions.
The Lord of the Rings Strategy Battle Game groups all "factions" into "Good" and "Evil" sides, and everyone in a side always work together. Most players, however, are expected to come up with some justification for why the different factions in their armies are working with each other.
While not always evil, per se, the monsters in the countryside of Final Fantasy XII are, despite being feral beasts, very very capable of teamwork. When they're of the same species, like Wolves, that's fair enough. When it's a Wolf, a Crocodile, and a T. rex simultaneously, it sticks out. (Although the T. rexis likely to eat the wolves and crocodiles.)
Subverted in the last dungeon of the first chapter of Neverwinter Nights 2. The Warlock and his demon army are battling against the Githyanki and against you as you wander through the caves.
In the Moria expansion, while you won't see any enemies fighting each other, paying attention to the quest descriptions will show that there's no happy family here. The Moria orcs are ruled by Mazog, but they are by no means the only orcs in Moria. Sauron has sent a number of orcs from Mordor there, and Saruman has sent emissaries to Moria himself, both of them trying to bring the local orcs under their command. A number of questlines deals with this, where your character is tasked with doing things that will make the orcs of the different factions fight each other, instead of joining forces.
Another example occurs in Goblin-Town. Orc-emissaries from Angmar are there to suggest an alliance between Angmar and the goblins of the Misty Mountains. Their offer is turned down in a homage to 300.
Bhoghad, Emissary to Goblin-town: Goblin, this talk is foolish. It is pointless. We are the army of Angmar. To defy our might and our strength is... madness! Ashűrz the Great Goblin: Madness? Madness? You fool! This is Goblin-town!
Both played straight and averted in City of Heroes. There's quite a few places where you can see villain NPCs of different factions fighting each other, sometimes to the "death"... But if you try to jump in, all of them will gang up on you.
Ditto for City of Villains. About half the missions you get will have you beating up other villains, with the remainder divided between beating up heroes and/or working for other villains.
Likewise is Dissidia: Final Fantasy, in which all of the heroes and all of the villains are aligned into two factions. Though, while they officially all belong to Chaos, there are plenty of sub-factions and personal plots involved. In its simplest form, the Emperor has a naked disdain for the "destroy the world" villains (like Exdeath and the Cloud of Darkness), Golbez is playing all sides, and nobody works well with Kefka.
Averted in Halo; the Covenant, the Flood, and the Forerunner Sentinels may all be trying to kill you, but they're also trying just as hard to kill each other. In Halo 2, the Covenant itself devolves into civil war as fighting breaks out between the Elites and the Brutes and they're happily tearing each other apart even as they try to kill you; in the last part of one level, Cortana even encourages you to hang back and let them finish each other off, though on the higher difficulty settings the Elites and Brutes will actually stop fighting each other in order to try to kill you.
Also averted in the setting as a whole; not only do the various races of the Covenant hate each other for the most part, but even sharing the same species is no guarantee of solidarity, with backstabbing and assassinations being the norm in political life.
It's played straight in Halo 4 with the Covenant remnant and the Prometheans, though the two sides only stop fighting each other when the Didact retakes control of the latter and allies with the former.
In Warcraft III, we have that neutral hostile is one happy family. All different creep races may work together depending on the map. Some pairings made some sense, like Ogres and Trolls (as a Call Back to Warcraft 2). Other pairings were not so logical, like usually placing trolls to support Magnataurs or golems.
Averted in Siren 2, where the Shibito and Yambito often attack each other and prioritize doing so over attacking humans. There are several levels where you can take advantage of this to sneak past enemies.
Averted in Metroid Prime 2: Echoes. Scanning various Space Pirate terminals reveals that the Space Pirates are having a hell of a time trying to fend off both Ing attacks andDark Samus. Dark Samus is also seen at one point hanging back to allow Ing to attack Samus, and at another mercilessly blasting her way through Ing standing between her and Phazon.
Semi-forced in the Warhammer Online MMO. Granted, it's not unheard of for the forces of Chaos to use the Orks as pawns, or the Dark Eldar to play everyone else for fools, or the Orks to join up with either side for the chance at a good fight; it's just extremely unusual for any of those factions to get along with itself long enough to form a grand scheme, let alone all three forming a coherent army big enough to get the humans, dwarfs and high elves to get together and form a massive alliance. Although explained away as basically a Gambit Pileup, it's pretty much understood that a "good versus evil" scheme is easier to implement than a "humans, dwarfs and elves only kinda-fighting each other versus Chaos versus Dark Elves versus Orks versus all the NPC things".
Averted in Doom. It only takes one or two stray shots to get a roomful of enemies (of different types, though bullets are fair game) to kill each other instead of you. In-universe, Cacodemons and Barons of Hell hate each other so much that they turn each other into bloody decor. Cacodemons go so far as to crucify Barons of Hell even though they don't have hands.
Averted in Iji, where the two alien factions actually prioritize killing each other above killing the player.
Averted in Blue Dragon. Putting certain enemies together in a fight will result in a Monster Battle, where the enemies will attack and kill each other before turning on you.
Endemic in the backstory of Fall from Heaven, where the reason the evil gods are evil is precisely that they all agree the world is a failure and that they should work together to prove that by corrupting it. The good gods have no reason to cooperate and generally don't get along that well. In gameplay, evil factions get a nice diplomatic bonus with each other (though that's mostly so that they'll be fighting the good factions rather than each other - good factions get the same bonus with each other), and that's just the visible one - there's also an extra hidden modifier that make them respect each other for being warmongers.
In The Legend of Zelda, every single enemy will attack you and not each other. This sticks out when you're fighting an Octorock, a bat-like Keese, and a blobby ChuChu at the same time, and all they're focused on is you.
Pokémon Mystery Dungeon is very guilty of this. Enemies even seem to form their own teams, following each other and attacking you just for being on the floor. Also, the backstory is that the earthquakes and other natural disasters have made wild Pokemon go mad, and attack the 'friendly' Pokemon that go into the naturally made caves, but only the Pokemon that enter, not the ones that were already there. There are even 'Monster Houses' where, upon entering the room, the games shouts at you "It's a monster house!" and about fifteen to twenty Pokemon drop from the ceiling and all attack you, even if it contains multiple Pokemon species.
Averted and then played straight during many "Crime In Progress" events in Batman: Arkham Origins, when, as Batman, you encounter warring gang factions who instantly resolve their differences so they can all attack you. This can result in, for example, both mobsters and corrupt SWAT teams shooting at you simultaneously. Justified in that if Batman wins, they all lose, so it's just common sense to aim at the most dangerous target.
The three fiends name the trope because they aren't at all inclined to work with Xykon — even though, as embodiments and champions of evil, fiends actually have a reason to want evil itself to win, whereas most evil characters simply want to advance their own ends by evil means. This both defies the trope and, in a way, plays it straight: the species of fiends are divided by war, but these three are working together (and almost seem to like each other) in spite of this, because they understand how much the war holds them back. At the same time, they are not going to help other evil guys further than what is useful for them.
Redcloak brought to Jirix's attention repeatedly the fact that Xykon, while a powerful ally, is more of a "rabid mammoth currently running in a right direction" sort than "good friend" sort.
Tarquin, for his part, seems to enthusiastically embrace the trope as part of being Dangerously Genre Savvy. Despite all being evil and having distinct ultimate goals and values, his adventuring band has remained together through thick and thin for decades and have set themselves up as shadow leaders for an unending series of puppet empires. They appear to be genuine friends in addition to being colleagues.
The PVCC of Sonichu infamy functions as this, in their never-ending quest to keep Chris from getting laid.
Abyssals from Bibliography instinctively work together even if their pre-descend selves were enemies.
G.I. Joe started with Cobra Commander leading the Cobra organization with agents such as Destro, The Baroness, Tamox and Xamot, and Zartan at his command. Over time, each one of them would get episodes where they would put their own plans into action to wrest control of the organization, eventually leading to the creation of Serpentor, an Even Bigger Bad who would eventually wrest control of Cobra entirely.
The Masters of the Universe toyline later created two more evil factions: the Evil Horde, whose whole purpose was to avert the trope (they were even more against Skeletor than He-Man) and the Snake Men, who played it straight in the original toyline yet averted it in the 2002 version.
This is also a very common trope on shows with a number of recurring Villains-of-the-Week; the first season or two has some bad guys with crappy schemes that get beaten by five spunky multi-ethnic teenagers and their Deus ex Machina, so the bad guys figure they can pool their resources, usually in a season finale. Usually they will be under the leadership of whichever baddie is the most conniving; occasionally a new extra-powerful villain will show up to unite them all. On Captain Planet and the Planeteers, when Zarm the God of war, played by Sting (and later replaced by Malcolm McDowell) got pig-guy Greedly, radioactive bermuda shorts guy Duke Nukem, evil science chick Dr. Blight, rat-thing Skumm, and evil CEO ponytail guy Plunder together and everybody became One Big Happy Family. For a while.
Xiaolin Showdown features some problems with the alliance between Chase Young and Wuya (namely, she has Chronic Backstabbing Disorder), but by the end of the third season, they've decided to stop arguing and stay together for the sake of Evil. Parents of the year, they're not.
Happened once in SWAT Kats. After realizing that their goals are pretty much the same, Evil Overlord Dark Kat and Mad Scientist Doctor Viper decide that they should work together, and even decide to recruit the Mange couple. Dark Kat called off the division of spoils -splitting the city- after the good guys were caught but before they were dead. That never works. The Manges had also cut a deal with Viper for him to remove DK's control collars from them because they suspected Dark Kat might doublecross them.
Played with in Kim Possible, mostly centering around Doctor Drakken, the resident loser Mad Scientist. Super-villainy itself is treated as an entire sub-culture with its own clubs, magazines, and Hench Co. Industries, a private enterprise supplying henchmen and gadgets for a price. Drakken, being an Ineffectual Sympathetic Villain whose schemes always fail, is usually too poor to afford that kind of stuff, so he ends up stealing from Hench Co. and other villains, notably his Always Someone Better rival Professor Dementor, though even then in their very last scene they are actually having coffee together. Then there are villains who actually are family: the Seniors are a father-and-son villainous duo, and Drakken himself is a cousin of evil mechanic Motor Ed. In the finale he finally ends up hooking up with Shego. They aren't the only evil couple to show up either.
Young Justice is more "Evil Is One Big Loyal Conspiracy with a Common Goal." Nearly every major villain in the entire series is either a member of The Light or an agent of The Light. Some might be out of the loop, but generally they are all in alliance with one another to some extent. Even some of the villains who don't like each other (Sportsmaster and Cheshire; Icicle, Sr. and the Riddler) often turn out to be allies through their connections to The Light. As this is a series where even The Joker and Lex Luthor are team players, it seems that The Light has managed to convince every supervillain on Earth to work together for their mutual benefit. Particularly notable that every single member is loyal enough that nobody has confessed any knowledge of The Light to an outside authority or otherwise betrayed The Light to any major degree.