One story arc has Cap teaming up with the Red Skull of all people in order to stop a resurrected Hitler from taking control of the Cosmic Cube. Incidentally, this would lead Cap to being briefly exiled from the United States, since the U.S. government assumed he had turned his back on America by aligning with the Skull.
Another time, Diamondback of the Serpent Society sought Cap out when the Viper (Madame Hydra) instigated a hostile takeover of the Society so she could use them to turn the population of Washington, D.C. into Snake People. The Captain and his allies helped Diamondback and other Society members still loyal to its founder, Sidewinder, in stopping Viper and reversing the effects of her snakeification of the Capital. This led to Diamondback's Heel–Face Turn and Sidewinder's retirement.
Doctor Doom: Doom and Kang cooperate briefly. They insult each other constantly, but respect each other's intent to kill the other at some point.
After the death of the Human Torch, Doctor Doom and Reed Richards have very reluctantly agreed to work together in the Future Foundation. This arrangement was brokered by Reed's genius daughter Valeria who convinced Reed that the FF needed someone as ruthlessly pragmatic as Doom if they were going to save the world. She got Doom on board by promising to help undo the brain damage the Intelligensia inflicted on him in Fall of the Hulks.
Not the first time Doom has teamed up with his enemies. An early story arc had him actually leading the FF against the villain known as Over-Mind.
One What If? comic had Wolverine, Spider-Man, Hulk and Ghost Rider take up the mantle when the original FF were killed. When a villain nearly kills them too, Doom shows up and saves them, declaring that no one, save Doom, may defeat the Fantastic Four... Apparently including their replacements.
Infinity: A large number of nominal enemies — including the Kree, Skrull, and Shi'ar empires, as well as the Avengers — unite to counter the threat that the Builders pose to the whole universe.
Kid Colt (2009): The main antagonist of the series, 'Bounty killer' Sherman Wilks, joins forces with Kid Colt when both sides are ambushed by scavengers. Some of Wilks' men aren't too happy with that arrangement, but the scavengers kill them before they can complain too much.
Loki is willing to fight on Thor's side pretty much any time Asgard is under attack; his goal is to rule it, after all, and he can't rule it if it's demolished. Also, in the Spider-Man comic "The Coming of Chaos", he was willing to team up with Spider-Man in order to save his mortal daughter, who had become possessed.
Secret Invasion (2008): The villain mastermind The Hood sends his forces into battle to save the Earth from the Skrulls. He has his own reasons for this: it helps Norman Osborn in his ploy to take over SHIELD and instigate the Dark Reign. (It's also implied that the Hood had no idea of Osborn's plan, until he called together the Cabal for the first time. The Hood would have let the assembled forces fight the Skrulls, if not for the simple fact that if the Skrulls destroy the Earth, they destroy his business.)
Spidey and Doc Ock ended up working together at one point, in order to deal with a new villain (Carlyle) who used Ock's arm technology to build a bank-robbing powersuit. While simply being robbed wouldn't have been enough to put Ock on the side of his mortal enemy, there was also the fact that Carlyle was threatening Ock's former fiancée, known to Spider-Man fans as "Aunt May". (Truthfully, Aunt May being endangered wasn't really a factor in the fight. It didn't do anything except surprise Doc Ock for a moment and lead to a very funny The Rocky Horror Picture Show joke. Spidey came into the fight late as Doc Ock was already going after Caryle for stealing his tech and trying to kill him. To Doc's credit, he DID stop a building from collapsing just long enough to allow the innocent civilians to escape at Spidey's prompting. That did nothing to STOP him from letting the building collapse on Spidey, noting "you are not a civilian". Doc Ock also wasn't happy about the inadvertent team-up, later noting (as he told Spidey the weakness in Caryle's armor), "I am not helping you — I am hurting him." World of difference.)
It wasn't even the first time Spidey and Ock teamed up, since they also set aside their differences when Hammerhead kidnapped Aunt May. Spider-Man wanted to rescue Aunt May because she was one of his loved ones (along with the fact that he was Spider-Man after all), while Doc Ock wanted to marry May so he could gain access to a nuclear power plant she had inherited.
Venom and Carnage hate each other far more than they hate Spider-Man. Any time Carnage pops up, Venom will call a truce with Spider-Man to go whale on Carnage. This most famously occurred in the storyline Maximum Carnage, which was adapted into a Sega Genesis and Super Nintendo game. Also, in the oddly-named "Venom vs Carnage" comic, after Carnage produces a new symbiote, he and Venom decide that, in the end, they hate the new symbiote even more than they hate each other (it's implied in Carnage's case that this is part of symbiote biology). The result? Their only teamup. Venom calls it "Temporary. VERY temporary."
In one of the most memorable stories of Inferno (1988) that didn't involve the mutant teams in the main storyline, Spidey fought alongside J. Jonah Jameson to defend the Daily Bugle against the invading demon horde. It was little wonder that the writers named the story "When the Bugle Blows!".
In the one-shot comic Spider-Man Dead Man's Hand, Spidey and his old enemy the Tinkerer cooperated for mutual benefit after the third Carrion infected New Yorkers with a disease that made them zombie-like minions. (The Tinker was working on a teleportation device for the Enclave that Spidey needed to get to Wungadore quickly, as he knew the High Evolutionary might have inside information on the plague, and the Tinkerer was willing to help, seeing as his son was one of the victims of said plague.)
Spider-Woman: Spider-Woman called a truce with several former enemies to escape the clutches of the Locksmith in the 50th issue of her series, and even invited a few of them to her apartment later! (Unfortunately, said party was interrupted by the darker threat of the story.)
Ratchet and Megatron teamed in an early episode to bring down Shockwave. Megatron, naturally enough, tried to betray Ratchet, but Ratchet was prepared.
Several years later, during the "Space Pirates!" story in the UK comic, the Autobots and Decepticons join forces to repel the Quintessons, who are trying to conquer Cybertron before Quintessa explodes. Ultra Magnus and Soundwave even get a Back-to-Back Badasses moment. At the end, Soundwave briefly considers the idea of a lasting peace, but realizes the two factions have come too far to ever resolve their differences.
Another storyline had Starscream come in contact with a cosmic power source called the Underbase, which made him so powerful — not to mention drove him to madness — that the Autobots and Decepticons were forced to team up to stop him. Notably, they were not able to — overdosing on the Underbase's power eventually destroyed Starscream.
Toward the end of the series, Optimus Prime actually surrendered to Scorponok in order to convince him that the two sides need to team up against Unicron, who was now on his way to Cybertron thanks to the accidental awakening of Primus. Scorponok wasn't entirely convinced until Primus himself teleported all the Earth-bound Transformers to Cybertron for the final stand.
In Transformers: Generation 2, the Autobots and Decepticons were forced to team up again against the Cybertronian Empire, a faction of hyperevolved Decepticons who had abandoned Cybertron eons ago to create a star-spanning empire of their own. They consider the Autobots and the original Decepticons to be disgusting savages, and eventually returned to destroy their "lesser" brethren.
Miles Morales makes an unexpected team-up with Rhino when he finds out that they are both following the same kidnappers. Also, Rhino may have had some fights with the original Spider-Man, but has no beef with this new one.
Ultimate X Men: The Brotherhood rescued the X-Men from Weapon X and joined forces against them. They defeat all the soldiers, but then disagree on what to do with them. The Brotherhood wants to kill them, but the X-Men think that If You Kill Him, You Will Be Just Like Him!.
X-23: In Vol. 3, the Daken and X-23 crossover involved this. Daken was initially working with Malcolm Colcord, while playing all the other parties against one another in pursuit of his own goals. However once Colcord's intent to recreate Weapon X is revealed, Daken and Laura throw in together to bring him down. Unlike Daken's relationship with their father, the team-up results in them becoming Friendly Enemies when they realize they're not so different.
X-Men: Magneto, always referred to as the Big Bad, is the first person the heroes team up with when someone worse comes along.
Particularly in the 90s cartoon, most notably in a season-long storyline in which he and Professor Xavier are stranded together in the Savage Land.
The brilliant X-Men graphic novel God Loves, Man Kills was the basis for X2, and thus follows the same plot except that, since the comics have been going on long enough that they didn't feel the need to hammer home his villainy, Magneto doesn't really have a Snap Back the way he does in the movie.
And in God Loves, Man Kills II, released to tie in with X2, the X-Men find themselves teaming up with the villain from the original.
Magneto has worked with the X-Men in multiple story lines, even becoming the leader in one story arc. This is because, for most writers, Magneto isn't as much a bad guy as he is a Well-Intentioned Extremist.
It wasn't just for one arc. In the late 1980s, due to Charles Xavier being absent, a reformed Magneto took over Xavier's School for Gifted Youngsters for something like four years (in real world time). If you were reading X-Men and New Mutants back then, Magneto as the head of the Xavier school felt like a new status quo.
When Nimrod the Super Sentinel started attacking everybody, the X-Men and the Hellfire Club had to work together to defeat him.
