Phil Foglio's graphic novel adaptation of Robert Asprin's Another Fine Myth features a Law Machine from his own Buck Godot: Zap Gun For Hire universe:
Aahz: "That was our introduction to...the Law Machine. We were all dimensional travelers...I haven't seen a Law Machine before or since."
Archie Comics is not afraid of this. The only real thing that defines the universes (excluding Sonic the Hedgehog and other licensed series) is different towns in America. The Archies performing alongside Josie and the Pussycats? Sure!
Sabrina, however, did cross over with Sonic the Hedgehog, in a two part-special that expanded both series.
In fairness, the early 1990s Frank Castle was essentially a well-equipped assassin, not an amoral wholesale slaughtering machine leaving dozens of bloody corpses everywhere. And he not only engages in less violence here than in his usual missions of the time, but he even lets his target live. Still, the fact that everyone involved managed to pull it off at all, much less make a pretty good story, is downright amazing.
In the 1990s, DC and Image published a crossover between Batman and Spawn. It's best remembered for completely rejecting the usual "meet, fight, become friends" routine found in most crossover comics. The two heroes hate each other for almost the entire story. At the end, Spawn wonders aloud whether they could try to be friends, and Batman responds by burying a batarang in Spawn's face.
There were a couple of stories in which Batman teamed up with Spider-Man.
Bongo Comics produced a mini-series called The SimpsonsFuturama Crossover Crisis. The first half is the Planet Express crew being sent into an issue of The Simpsons by the Brain Spawn. The second half is the residents of Springfield being pulled into New New York by one of Professor Farnsworth's inventions. And then it gets weird...
At one point, they also did a string of Slice of Life segments during commercial breaks where all of the characters were shown coexisting in some sort of vaguely defined urban setting.
A special magazine published in 2000 by Cartoon Network featured a five-page comic story in which Scooby-Doo meets The Powerpuff Girls. Bubbles, as expected, glomps Scooby ("Puppy!!").
G.I. Joe and Transformers. While the TV show is limited to the "Old Snake" thing and the hologram of Marissa's dad (see Western Animation below), the comics have crossed over many, many times, even to the point of very important and far-reaching events in one starting in crossovers such as Cobra being the source of Megatron's tank body, and Bumblebee getting blown up real good and later repaired as his new Goldbug form - though if you're from the UK, you got a different Goldbug origin.
Various Image Comics titles (Invincible, Savage Dragon, Witchblade, etc.) occasionally cross over, but the editorial policy is that what happens in one title doesn't have to affect events in another. Each hero lives in his or her own unique universe that may or may not contain versions of the other heroes. For instance, Invincible's universe has a Savage Dragon and a Witchblade who are more or less the same as their counterparts in their own books and have roughly the same adventures, but what happens in Invincible's book stays there.
That is the main premise of the IDW comic Infestation: Outbreak, where a dimensional gate (which looks suspiciously like a Stargate) unleashes hordes of zombies from another world. Unlike other zombies from this world, these are guided by a single will, the Undermind. They are also somehow capable of infecting technology and other undead creatures. When an elite vampire squad is sent to deal with the situation, one of them, Britt, gets bitten and becomes a vampire/zombie hybrid. Britt uses artillica to open four more dimensional portals, through which the zombies and infected machines pour, along with parts of Britt herself. While the other vampires manage to shut down the portals, the threat has already spread to other worlds. These worlds are those of G.I. Joe, Star Trek, Transformers, and Ghostbusters. All these worlds now have to fight an infestation from a virulence they have not seen, infecting both man and machine.
Infestation 2 had the Elder Gods invade the IDW Teenage Mutant Ninja Turtles, G.I. Joe, Dungeons and Dragons, Bat Boy, 30 Days of Night, and the Transformers: Hearts of Steel universes by creating a rift through universes through H.P. Lovecraft's writings.
A January 2014 IDW comic also had The Ghostbusters being investigated by The Lone Gunmen from The X-Files.
José Carioca's universe is set in his home country of Brazil, but he's shown to be friends with Donald Duck in Saludos Amigos and The Three Caballeros (as well as the ride in the Mexican pavilion at Epcot). Thus, there are occasional crossovers between the Carioca universe and the McDuck Universe. Indeed, there has been a prolonged arc of stories where José visits Duckburg, and interacts with the various characters there.
The Incredible Hulk has crossed paths with Superman and Batman}} in separate issues.
Superman and Batman have been appearing in comics together since the Silver Age, and Wonder Woman joining in isn't rare, either. Generally they team up, though having them fight each other is always a good way to draw in readers.
Superman: "We're surrounded, you know. I can hear them all."
Batman: "I think we can take them. Do you think we can take them?"
Usagi Yojimbo and Teenage Mutant Ninja Turtles had several single-issue gag crossovers in their respective early runs, which culminated, several years later, in a volume of Usagi which centered on a village shaman summoning the Turtles to fight invading ninjas, and the Turtles' subsequent confusion at being landed in a medieval Japan inhabited by talking animals.
The various Marvel–DC crossovers that have been published over the years, which imply the existence of a third timeline separate from the Marvel and DC continuities in which both exist alongside each other.
There was also the Amalgam Universe, which consists of heroes who merge traits of a hero from each universe. Examples are IronLantern (take a guess) and Darkclaw, who was Batman and Wolverine (!!!). However, the events of JLA-Avengers are taken as canon for both publishers in their mainstream universes.
The very first superhero crossover was a battle between the Human Torch and the Sub-Mariner in Marvel Mystery Comics #8 and #9 (1940). This is the beginning of the Marvel Universe.
Actually, the Shield and the Wizard at MLJ met earlier. The Wizard had learned of an impending attack on Pearl Harbor and contacted the Shield. They spent the next few issues fighting the same enemies (the Soviet/Nazi proxies called Moskovians), occasionally crossing paths for a panel or three.
In the German comic Werner: Dex & Dogfort appear in Volle Latte!, drawn by Jörg Reymann himself. In retour, Werner appears in the third Dex & Dogfort book, Schlachthofgiganten.
In the story about Wilhelm Busch's 150th birthday at the end of Alles klar?, Werner and Wilhelm Bush let loose his characters from Max and Moritz because they find the celebration boring.