Crossovers between characters owned by different companies ALWAYS go like this: they fight, they team up, and (due to legal reasons) they never mention each other ever again. Well, almost always. Some have managed to get around the logistical and inter-dimensional limitations of these crossovers with wonderfully WTF results, like ...
When famed writer/British person Warren Ellis was asked to write a crossover between the sexy superheroes from WildC.A.T.s and the dong-headed aliens from Alien, he thought the idea was "bloody stupid." He also said so out loud. Repeatedly. Then his editor added a little detail that changed Ellis' mind: he could kill anyone he wanted. Uh, in the comic. Hopefully that part was clear when he accepted the gig.
IDW Publishing, DC Comics
At the time, Ellis was writing another series called Stormwatch, but he was painfully uninterested in any of the characters except for a select few (as in, the ones he created). He was already planning to spin off his characters into a new series, but he still needed to figure out what to do with those other losers. Then a bunch of perfect killing machines from outer space fell on his lap and gave him the perfect excuse to get rid of them in needlessly gruesome ways.
DC Comics, Dark Horse Comics
Ellis gave so little shits about the Stormwatch gang that he didn't even show their deaths in the comic -- the WildC.A.T.s show up to help and stumble upon their corpses. Two Stormwatchers made out of energy were somehow turned into gas by the aliens and unknowingly breathed (then presumably farted) by their WildC.A.T.s pals.
And unlike most crossovers, the consequences of this one actually stuck. The next (and final) issue of Stormwatch opens with the funeral for the dead heroes while the survivors moved on to Ellis' critically acclaimed spin-off, The Authority. Stormwatch is now owned by DC, which means that all the dead characters have been rebooted back into life, but we like to think that their eye still twitches a little whenever they hear the words "Ridley Scott" or see anything even vaguely phallic.
The comics based on J.J. Abrams' excessively shiny Star Trek pseudo-reboot bridge the gap between the movies, showing Kirk and crew's encounters with cosmic menaces, strange alien races, and ... flying dudes in green spandex powered by magic bling?
IDW Publishing, DC Comics
In the comics, the Enterprise has bumped into everyone from the Transformers to Doctor Who, but what makes Star Trek/Green Lantern (2015) special is that it eschews the default "and then everyone went home and everything went back to normal" crossover ending. The Green Lanterns in this series come from an alternate version of the DC Universe where the Justice League sorta dropped the ball and let the embodiment of death kill everyone. So, since they have no home to get back to after the usual meet/fight/team up routine, some Green Lanterns join the Enterprise as crew members while others decide to fart around this universe, seemingly over the deaths of all their friends and family already.
IDW Publishing, DC Comics
The story continued a year later in an even nuttier sequel that involves Kirk gaining a power ring, Khan becoming a Red Lantern, and traitorous ex-Green Lantern Sinestro (WatchMojo's #1 least shocking anime betrayal) ruling the Klingons. Both series are written by the same writer of the main Star Trek comic, whose work was once declared canon by the movies' screenwriter. Therefore, unless the next movie starts with Spock looking at the camera and specifically saying "By the way, we have never met any Green Lanterns," it's our responsibility as obsessive nerds to assume that there was a guy with a magical ring just outside of frame in every scene of 2016's Star Trek Beyond.
The only hitch in our theory is that, in the crossover, Bones outfits the red shirt officers with knock-off Green Lantern rings for protection, but those are nowhere to be seen in Beyond. Maybe Kirk decided it just wasn't the same without ten of those guys dying in every mission and came up with some bullshit reason to take them away?
When Spawn debuted in the early '90s people talked like he was the next Batman, Superman, and Spider-Man combined -- surely this was only the beginning of several decades of total Spawn media domination! That super didn't happen, but Spawn did get to meet the real Batman in 1994 ... or at least the grumpy "Clint Eastwood in tights" incarnation of Batman, since the crossover was written by the also-grumpy Frank Miller.
In fact, the first thing you see when you open the comic is a note stating that this is a "companion piece" to Miller's The Dark Knight Returns series, and it "does not represent current DC continuity." It was important for DC that you knew that the official Batman didn't end every other sentence with the word "punk."
Image Comics, DC Comics
After Batman and Spawn spend 90% of the issue punching and insulting each other, they eventually move on to the obligatory team up part, which involves stopping some lady from turning decapitated hobos into killer robots. On the last pages, Spawn proposes leaving their differences behind and becoming buds. Batman, clearly moved by this gesture, decides to gift his new friend one of his world-famous Batarangs ... right in the middle of his face.
Image Comics, DC Comics
Image Comics, DC Comics
Normally, what happens in crossovers stays in crossovers, but in this case, the next issue of Spawn started with the character getting his face stitched together with a shoestring and talking about running into "some bozo in black." Later issues claimed the bozo was Harry Houdini (the closest thing to a public domain Batman), but the moment when Spawn debuts his shoestring look is clearly meant to evoke that Batarang panel:
Spawn kept the shoestring on his face for the next three years, after which it was worn by his ex-wife's daughter as a crappy necklace. Presumably he still has the Batarang, unless he had to sell it on EBay in the '00s when everyone stopped reading his comic.
In 2013, X-Files creator Chris Carter announced an official comic book continuation of the show, thus allowing fans to imagine how completely awesome and not-awkward and terrible it would be if they ever got a new season. One of the tie-ins to the comic was a crossover event involving the Ghostbusters, the Teenage Mutant Ninja Turtles, the Transformers, and the Crow, properties that were clearly chosen due to their affinity with The X-Files and NOT because the same publisher happened to own their license.
The crossover starts with Agent Mulder's conspiracy theorist pals, the Lone Gunmen, getting an e-mail from the future warning them that a virus is about to ravage the human race (out of all the implausible stuff seen in The X-Files, that's got to be the dumbest). In order to stop the virus, the Gunmen must investigate a bunch of weird shit included in the future e-mail, like sightings of humanoid turtles or talking cars from outer space.
These aren't, like, realistic stand-ins for the Turtles or the Transformers, like the time "Homer Simpson" showed up in an X-Files episode -- they are the real deal, in all their wacky Saturday morning cartoon glory. The issue with the Ninja Turtles is a sequel to both a storyline from the current TMNT comics and a classic X-Files episode. At least it was a somewhat pizza-related episode, so the tonal whiplash isn't that bad.
In the end, Scully creates a vaccine for the virus by combining the blood of the Ninja Turtles with the blood (oil?) of a Transformer, and the Gunmen find out that they're the ones who sent the future e-mail. This creates a paradox that erases the entire event from history, but the damage is done: now we know that giant aliens and mutants have always existed in the X-Files world, and Mulder and Scully absolutely suck ass at their job.
It's not uncommon for characters who look suspiciously like Marvel or DC heroes to show up in a comic from the other company, make an ass of themselves, and then never be mentioned again. This appeared to be the case with a 1990 Superman issue featuring four astronauts who gain fantastic powers after their shuttle is bombarded with cosmic radiation. The twist was that, instead of becoming superheroes like the Fantastic Four, these guys just slowly die of radiation poisoning.
What's surprising is that, in a roundabout way, this unofficial homage/dig at a rival company led to a crapload of actual crossovers between Marvel and DC years down the line. You see, the Mr. Fantastic ripoff, Hank Henshaw, later turned out to be alive, but he went crazy and started blaming Superman for the death of his wife. When it was Superman's turn to be dead for a while, Henshaw decided to ruin his good reputation by posing as an evil cyborg Superman imaginatively named "the Cyborg Superman."
To show how evil he was, the Cyborg Superman nuked an entire chunk of California called Coast City, home of Green Lantern Hal Jordan. This led to Jordan also going insane and evil (a popular superhero career choice in the '90s) and becoming a near-omnipotent supervillain called Parallax. While being chased around space by a pissed off Parallax, the Cyborg Superman gets sucked through a tiny rift into the Marvel Universe by Thanos -- it's never stated outright, but it's probable that the reason Thanos was able to pull the Cyborg into the Marvel side was that, well, he was already a Marvel character.
Anyway, the shenanigans between Thanos, Parallax, and the Cyborg result in a team up between Silver Surfer and Green Lantern (a different, non-evil one). All that back and forth between the universes causes that little rift to grow into a gaping multiversal asshole that directly precipitates 1996's DC Vs. Marvel mega-crossover. DC Vs. Marvel, in turn, spawned two sequels, 24 special issues merging characters from both universes, and a few other related crossovers ... including one between Superman and the actual Fantastic Four, released in 1999. The Cyborg Superman shows up there and has a little "huh, you look familiar" moment when he meets the FF.
DC Comics, Marvel Comics
In 2009, Mr. Fantastic met a Council of Ri-- er, Council of Reeds made out of versions of himself from different realities, and every single one of them turned out to be evil. The Cyborg Superman wasn't invited due to copyright considerations, but at least he can say that he predicted a plot twist in another company's comic almost 30 years ahead of time.
Top Image: IDW Publishing