In the 1970s, two issues of The Brave and the Bold featured Batman teaming up with The Joker to solve a crime. In #111, they worked together to solve the mass murder of an upstanding local family, which someone had sloppily tried to pin on the Joker. In the end, it turned out that the whole thing was an elaborate plot between the Joker and the killer to lure Batman into a Deathtrap. In #191, the Penguin is murdered and it looks like the Joker did it. When Batman catches up to him, he proves that he couldn't have done it. It is eventually revealed that the whole thing was a Faking the Dead by the Penguin, who used it to kidnap a local cardinal.
Discussed and then soundlydefied in Batman Beyond. When Man-Bat threatens the city with a sonic weapon, Terry believes Commissioner Gordon and Dick have called him to suggest he team up with Shriek, the other villainous sound expert, "just like in the vids". They respond by pointing out that Shriek is a madman and a loose cannon, and there's no way they could ever trust him. Terry seems quite disappointed to hear it.
"Caught in the Widow's Web"/"Batman Fights the Penguin's Dread" has the Penguin join forces with Batman and Robin to take down the Black Widow after Batman points out to Penguin that Black Widow is likely to kill him once she no longer has use of their partnership.
The crossover miniseries with The Man from U.N.C.L.E. has Batman's enemies Mr. Freeze, Scarecrow, Poison Ivy, Egghead, Siren, Sandman, and Olga, Queen of Cossacks team up with Batman, Robin, Batgirl, Napoleon Solo and Illya Kuryakin against Hugo Strange after Batman reveals to the villains that the heroes will outrank the villains in the T.H.R.U.S.H. hierarchy if the efforts to brainwash the heroes into serving T.H.R.U.S.H. are successful. However, this doesn't prevent the villains from betraying the heroes at the last minute.
While they might be opponents, Batman and Poison Ivy both unquestionably agree on one thing: they will not allow Harley Quinn to become a victim of the Joker's abuse again.
In Crisis on Infinite Earths, Darkseid ended up being instrumental in finally defeating the Anti-Monitor (but making it very clear he was only doing it not to help the heroes or anything, but rather to ensure that the Anti-Monitor wouldn't destroy everything).
Darkseid did the same thing with Imperiex.
DCeased: The penultimate issue of the concluding miniseries DCeased: War of the Undead Gods has Darkseid team up with the heroes against Erebos after he is cured of the Anti-Life Equation and learns that he had been a pawn to Erebos' agenda all along.
Forever Evil (2013): Lex and his "Legion of Doom"-esque alliance fighting back against the larger, more encompassing threat the Crime Syndicate poses.
In Year Five of Injustice: Gods Among Us, Batman recruits several supervillains to help him fight Superman's Regime, choosing them based on their adherence to a no-kill rule. After learning of Batman's plan, Superman does the exact same thing, though the villains he chooses are willing to use lethal force and are thus more numerous.
Jonah Hex: In #10 of the original series, el Papagayo forces Jonah to aid him in a plan to steal a store of gold from the Mexican government. When the the soldiers uncover the plot, they assume Jonah is a willing participant and Jonah is forced to fight alongside the outlaws to save his own life.
In the final issue of Paul Cornell's Knight and Squire, everyone in the British super-community teams up to take down The Joker. The heroes, the anti-heroes, the Harmless Villains and the killers like Death Dinosaur. He's just that much of a threat.
In The Multiversity, Superdoomsday wrecked havoc on several Earths, but because he and his fellow Overcorp stooge are the only champions of Earth-45, Harbinger is forced to summon them in the final battle alongside several superhero teams he had previously wronged. Members of the Earth-10 New Reichsmen and Freedom Fighters are likewise recruited. However, due to the sheer immensity of the conflict, these antagonistic groups have little opportunity to lock horns.
Supergirl had to reluctantly join forces with Blackstarr — one of her worst enemies — during the Crisis on Infinite Earths.
In The Girl with the X-Ray Mind, Supergirl and Lex Luthor are forced to team up twice. First, Luthor warns Supergirl about a criminal gang -who are trying to recruit his little sister so Supergirl can stop them before they ruin Lena's life. Supergirl cannot help but feel surprised by this development. Later, Supergirl talks Luthor into helping her stop the Phantom Zoners by pointing out their scheme is endangering Lena's life.
Supergirl: I never dreamed that some day Luthor would ask my help against the underworld!
At the end of Final Crisis, Superman is facing the Female Furies and the Justifiers. Who saves him and reverses the Anti-Life Equation? Lex Luthor and Dr. Sivana.
Lex:"Not a single word, Superman. We'll call this the Historic First Team-Up of the forces of "Good" and the forces of "Bad". And I'll take the credit for the win" Superman:"Whatever you say, Lex. Whatever you say."
Superman and Lex Luthor are in conflict almost all the time, and loathe each other with a vengeance, but they have put aside their differences, abandoned their other objectives, and teamed up to take down villains bent on destroying Metropolis more than once.
In Superman/Doomsday: Hunter/Prey, Superman teams up with Darkseid to stop both Doomsday and Cyborg Superman as they both attack Apokolips.
The Great Phantom Peril: During the final battle, Faora commands the Phantom Zoners to attack Superman. Neither of them likes being ordered around by her, but the Zoners hate Superman more than they despise Faora.
Faora Hu-Ul: "Hear me, males! Kill him where he stands!" Kru-El: "We're obeying Faora?" Dru-Zod: "Destroying Superman must not be our first priority!"
Two for the Death of One: When Lord Satanis realizes his power is not enough to beat Syrene, not even after taking over Superman's body, he asks Superman's subsumed consciousness to awaken and help him fight her.
Lord Satanis: "It is no use. I fight... But my powers are not nearly great enough! Superman, whatever part of you that can still think and resist... I call to you now! Aid me now, venerable foe — Or both of us shall surely perish!"
The Planet Eater Trilogy: Brainiac cannot stop one of his out-of-control creations, so he must team up with Superman to stop the Planet-Eater before it destroys everything.
Brainiac:"To think, my own creation nearly destroyed me! And now, to stop it before it destroys all living matter throughout the galaxy— I must seek the aid of the man who was once my most dreaded foe!"
Watchmen: This was the driving force behind the ending.
Wonder Woman (1987): Deathstroke unhesitatingly joins up with the heroes to fight Circe and her rather large collection of female villains gathered to hunt men, specifically superhero men, for sport in New York City.
