Part of the Red Ribbon Army story arc on Dragon Ball had Goku chasing Captain Blue to Penguin Village, the setting of Akira Toriyama's earlier manga/anime, Dr. Slump, and featured appearances by Arale, Dr. Norimaki, and several other characters. This appeared in the manga and anime (since both shows were made by Toei and aired on Fuji TV); moreover, when Dr. Slump was animated again in 1997, a new Dragon Ball crossover was written in.
Toriyama already did that in Dr. Slump itself: there was one chapter where the characters traveled to Wonder Island, the set of the titular manga (and Toriyama's very first published work).
That the author of Flunk Punk Rumble's favorite author happens to be the author of Fairy Tail probably helped, as well a former assistant of his. What's most stunning of all is that despite being SERIOUSLY WTF, it actually ain't half bad.
Fairy Tail also had a crossover with the story Mashima wrote before it, Rave Master. The Jiggle Butt gang appeared in the anime as well.
At one of the Jump Fiesta events they featured another crossover of Luffy and Goku going up against Eneru above the city of Tokyo. Other characters get short cameo and Ryotsu of Kochikame made an appearance (as seen here). They would later do this again only this time against Arlong and Astro Boy was thrown into the mix.
Rodimus's backstory in Transformers Energon states that he left Cybertron with a band of Autobots and "traveled into the future", which reflects the ending of Transformers: The Headmasters, in which he ventures off into space to find/found a new home planet.
It's not much, but in G Gundam, during the finale episode where all the world's Gundams had banded together to fight the Dark/Devil Gundam, you can see Gundams from other series in the mob. For example, both the standard RX-78-GP01 and the RX-78-GP01 Full Vernian, the Wing Gundam, RX-78-2, etc. They weren't kidding when the said they had all the Gundams!
In-universe example in Bakuman。: Crow and +Natural are two manga drawn by the same artist, the former about a crow-man (or something like that, the premise is never stated), while the latter is about a kid who finds he's psychic. Fast forward to a time where +Natural is doing poorly while Crow remains among the most popular of Jump, and you get the protagonist of Crow showing up in +Natural, saying he's also a psychic. (We only know so much about the Shows Within A Show, so we can't be sure that they're in different continuities, but given the plots and the characters' reactions, this seems to be the case.)
This has become a recent trend with Shonen Jump manga, and the anime adapted from them.
Gintama and Sket Dance had a crossover chapter for each manga, and two corresponding crossover episodes.
Toriko and One Piece had two crossover episodes (one of which was adapted from a manga crossover).
And, most recently, One Piece, Toriko, and Dragon Ball Z'' had a crossover episode, though it obviously had no bearing on the continuity of any of the anime involved.
The Doctor showed up in one of the Buffy Season 8 comics for a panel (along with Rose). Suddenly London's forgetfulness makes sense.
Beginning with Predator vs. Aliens, the two extraterrestrials have done battle (either one-on-one or multiplayer deathmatch) with essentially every superhero ever created, no matter how illogical the match-up. Taken to ridiculous extremes in Superman and Batman vs. Aliens and Predator. Perhaps the most famous of these stories was WildC.A.T.s/Aliens which actually had an impact on the former's continuity and saw the deaths of several members of Stormwatch to allow Warren Ellis to clear the decks to create The Authority.
Despite their rivalry, DC Comics and Marvel Comics have had numerous crossovers between their two companies, leading to meetings between Superman and The Mighty Thor and in particular Batman and Captain America, the two companies main Badass Normal heroes, and also confrontations between heroes and villains from each, such as Spidey taking on the Joker. The whole thing even has a standing Hand Wave established in the late 1990s, that the Marvel and DC universes will occasionally start to merge on their own, leaving teams from the two inhabiting the same continuity all of a sudden and remembering each other as if it's always been that way. For instance, in the X-Men/Teen Titans crossover, at one point they even discuss bringing in the Justice League and Avengers to help.
An interesting example: X-Men and Teen Titans◊. Starfire learns languages by kissing people, and Nightcrawler thinks that's terrific.
Judge Dredd has teamed up with Batman on at least three occasions; given Bats' vigilante status and Dredd's fascist asshole status, there was some distinctly Teeth-Clenched Teamwork on both sides. Dredd has taken on Aliens and the Predator as well. And in 2000 AD publications themselves, Dredd has crossed paths with Johnny Alpha from Strontium Dog twice (Both of these strips have been created by the same people) and has seen a whole score of cameos from outside characters during the Helter Skelter story arc.
One of the single most bizarre intercontinuity crossovers, ever: ArchieMeetsThe Punisher. Even more bizarre? It's not that bad. The Archie EIC at the time admitted the comic came about from him randomly meeting some Marvel guys at a cafe and talking.
Illyria of the Buffy Verse has appeared in Peter David's Fallen Angel. David also wrote an earlier Illyria-one-shot.
Top Cow had an extended crossover with Marvel where the companies' characters live in different universes and which is probably in continuity, although several crossovers are pointedly not (like the one where Wolverine gets married to Sara Pezzini), and a Darkness/Batman crossover which featured an important in-continuity event that affected the Darkness series itself, even though it couldn't possibly be in continuity.
Captain Atom: Armageddon thrusts the DC Comics hero into Jim Lee's Wildstorm universe. The mini-series functions as a Cosmic Retcon for Wildstorm, and allows those comic readers who generally hated the ridiculousness of The Authority watch them get their heads handed to them.
Mars Attacks! the Image Universe!The Savage Dragon actually kept it in-continuity, with an issue that gave a basic overview for those who didn't read it, and continued the story from there with Chicago recovering from the invasion.
When it was originally planned as a four-issue limited series, Transformers shared the same 616 universe as other Marvel characters. J. Jonah Jameson sent Peter Parker to Oregon to investigate the Transformers (he wanted pictures of Optimus Prime) and thus Spidey and the Autobots teamed up. When the title became a monthly ongoing series, however, the crossover was quietly forgotten. The Transformers letter column even asked fans to please ignore the earlier Marvel crossover stories. However, after it became a regular series, the character Circuit Breaker appeared in Secret Wars II, issue 3, indicating some connection between the series and Marvel continuity.
A company crossover between IDW and Marvel did have the Avengers and Autobots team up. It's considered ambiguously canon by IDW.
They also, naturally, had crossovers with their G.I. Joe comic, to the point that in the "Generation 2" series, they all but merged. Years later, nearly anybody with the license will consider making their own version of the crossover, notably Image's alternate universe which is set during World War II, and Devil's Due's 4-part series, which is actually referenced in the Titanium Series toyline.
The Fantastic Four piloted Combattler V once. This was when Marvel was publishing a Shogun Warriors comic book under license from Mattel, who released several Japanese Humongous Mecha toys under the banner. The Warriors were fully integrated members of the Marvel 616 universe, though now that Marvel has lost the license...
Hack Slash has crossed over with several other horror series and characters, including Evil Ernie from Lady Death, Childs Play, Hatchet, BUMP, and Re-Animator. Tim Seeley, the writer, has said in interviews that he considers all slasher films to take place in the same universe of canon (justified by some of the entries in the cinema section of this page).
Star Trek / X-Men Almost certainly created so a scene where Bones and Beast were called to with "Doctor McCoy, and both would answer "What?"
The first Vertigo Comics Winter's Edge special has a House of Secrets framing story where Rain visits an art gallery in the house that shows her stories from The Sandman, The Books of Magic, Hellblazer, The Dreaming, The Minx, Nevada and The Invisibles. While the first four are part of one continuity, the latter three are all individual continuities, as is House of Secrets itself.
The two House of Mystery Halloween annuals may count, because each features a story from iZombie, which hasn't been confirmed to be part of the main DC/Vertigo continuity, unlike House of Mystery and the other titles that appeared in the annuals (Madame Xanadu, Lucifer, Hellblazer, and The Dreaming).
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."
Batman crossed over with Grendel twice, with the two crossovers featuring different Grendels. Batman is canonically one of only two people (the other being Argent the Wolf) to be able to fight original Grendel Hunter Rose on equal terms.
Buffy the Vampire Slayer seems to be a bit of a crossover whore in fanfics. Crossovers include Halo, CSI: Crime Scene Investigation, every Batman continuity, Stargate Verse, and plenty of others. A lot of the Halo crossovers are YAHFs ("Yet Another Halloween Fic", referencing the season 2 Halloween episode in which everyone got turned into their costumes) where Xander becomes John-117; these have an odd tendency to become Stargate SG-1 crossovers at the same time. There are even a couple Animorphs crossovers, despite Buffy being referenced as fictional in the Animorphs books. Merlin naturally has some, due to Anthony Head playing main roles in both series.
The fanfic The Chronicles of the Nine Kingdoms is essentially all the Nintendo Worlds (with a few other worlds that have appeared on Nintendo systems, like Dragon Warrior Monsters) crossed over together with the Mario world as a centerpiece for a quest against evil. The author even takes it farther by planning to cross his fanfic with a Metroid fanfiction written by his friend.
Goku/Anne Frank: Until the End of Time. If the notion of a Dragon Ball Z/Anne Frank crossover hasn't made your brain implode already, wait until you get to the part where Hitler becomes a Super Saiyan.
Heero Potter, where Heero Yuy is Harry's son, Duo Maxwell is Duo Weasley, Trowa Barton is Trowa Weasley, and Quatre Raberba Winner is Quatre Malfoy. I never knew the After Colony years started sometime soon after Harry Potter allegedly ended.
Because of the popularity of a background character "Dr Hoof/Whooves", there are a swarm of crossovers between Doctor Who and My Little Pony: Friendship Is Magic. It is even the case that many fics that aren't an actual crossover will have the Doctor as a side character and more or less explicitly make clear that yes, he is the time-travelling alien beloved by fans; he just regenerated as a pony.
In fact, due to the popularity of Friendship is Magic, and very prolific fanfic writers, My Little Pony: Friendship is Magic has crossed over with just about everything, from The Dresden Files to Stargate SG-1.
Highlander attracts a lot of crossovers as well, mostly because there are many characters that it's easy to make immortals. Stargate SG-1 occasionally gets pulled in because of Peter Wingfield guest starring on SG-1. It also has been crossed with Buffy the Vampire Slayer due to both series having groups of Watchers.
Several arcs of You Got HaruhiRolled! feature characters from other series interacting with the Haruhi Suzumiya characters. The pirate arc has, as its villains, the main characters of Lucky Star. Chapter 86 has a story in which Batman and the Joker fight it out at a baseball game Haruhi attends. But it is the court case arc which goes Up to Eleven, operating with the conceit that all characters from every work of fiction ever live together in a single city, thus allowing for a Mega Crossover where characters from countless fandoms take part in Haruhi's trial in one way or another.
Randolph and Mortimer Duke from Trading Places — reduced to homeless poverty by the events of that film — show up in Coming to America. They fail to notice Prince Akeem's uncanny resemblance to Billy Ray Valentine.
As a random gag in the third act of Wayne's World, Wayne gets pulled over by a cop on a motorcycle… who turns out to be the T-1000, looking for John Connor. He shows up again in Last Action Hero.
In Casper, the bad guys attempt to de-haunt the house using the services of Father Guido Sarducci, and Dr. Ray Stanz from Ghostbusters. "Who you gonna call? Someone else!" (According to The Other Wiki there was also a scene filmed with Zelda Rubenstein (Tangina Barrons from Poltergeist) but it was cut.)
George of the Jungle ends with George holding George Jr. over the very same rock where Simba was similarly held. It's all Disney. And George kicked some serious lion's ass, so it could be canon.
The comic book Star Wars Tales #19 has an alternate history story where Han and Chewie crash-land the Millennium Falcon on Earth, where it is found 126 years later by Indiana Jones. Later, Industrial Light & Magic was hired to do the effects for Star Trek: First Contact, and some wiseguy at ILM snuck the Falcon into the Battle of Sector 001 as a Freeze-Frame Bonus/Easter Egg.
The basic concept of the Thursday Next books is that all novels are connected through the Bookworld, and Thursday can travel to them. For obvious reasons, the books Thursday enters are mostly public domain, but the cast of Enid Blyton's Shadow The Sheepdog, Beatrix Potter's Mrs Tiggywinkle and Kathy Reichs' Temperance Brennan have all appeared with permission. (Of the estates in the first two cases, obviously.)
The Doctor Who character Iris Wildthyme (see here for character tropes) started out in a wildly unrelated series of non-genre novels. The author proceeded to use her in Doctor Who novels with no change whatsoever to her character. She then got her own Big Finish spinoff and a number of appearances in the comics. Unlike with other not-quite-canon Doctor Who companions, Big Finish makes no effort to prevent a Continuity Snarl with her, and Iris somehow being part of several different continuities all at once is considered part of her charm.
Interestingly, there's an episode of Homicide in which Munch refers to people "watching The X-Files." You could take this as a paradox, or you could figure that Munch — a hard-core conspiracy theorist — leaped at the chance to play himself in an X-Files episode. Which might explain why the interrogation room in that X-Files ep looked completely different from the interrogation room in Homicide.
There is uncertainty over whether Belzer appears as Munch on The Wire; the character was not named and received a generic billing. He mentioned that he used to own a bar, however, which he did in Homicide, so there's some evidence that it was intended to be Munch.
Taken even further with Luther, in which the titular character tells a subordinate to check out an American felon by sending their profiles to Munch in New York. Celebrity Paradox kicks in, considering that the London cop John Luther and Baltimore gangster Stringer Bell in The Wire are both played by Idris Elba.
MTM shows did this occasionally. Carla from Cheers talked about having given birth at St. Elegius, aka St. Elsewhere, and the doctors showed up at the Cheers bar once. Sam also once directed patrons to take an ailing man to St. Elegius. Similarly, Bob from The Bob Newhart Show made reference to St. Elegius, while Bob's secretary Carol showed up on Murphy Brown as a temp for Murphy, thereby enfolding it into the autistic daydream which ended St. Elsewhere. See above for more information.
The Kaldor CityDoctor Who Expanded Universe audio dramas written by Chris Boucher and produced by Magic Bullet are set in the titular city from the Doctor Who story The Robots of Death (also by Boucher), but feature Scott Fredericks reprising the role of Psychostrategist Carnell from the Blake's 7 story "Weapon" (also by Boucher). The A History by Lance Parkin (an un-official history of the Whoniverse) makes a valiant attempt to claim that B7 may well be set in the Whoniverse, but really it's probably best to assume he's an Alternate Universe counterpart. Or just don't worry about it. (There's also a cynical manipulator played by Paul "Avon" Darrow, who knows more about Carnell's Federation background than the Kaldorians, but let's not even get started on that...)
Marvel also linked Doctor Who with Transformers, by way of bounty hunter (sorry, "freelance peacekeeping agent") Death's Head. This is a borderline case, however, as the linkage only occurred when Death's Head fell through a dimensional rift from the Marvel UK Transformers universe and ran into the Doctor as a result.
In a more solid (possibly) example, the obscure character Octus has been stated to have a Dalek altmode. He was never seen transformed, but Word of God says that's what he turned into.
It appears that the soap opera Passions has set itself up as a sequel of sorts to the classic Fantastic ComedyBewitched. It features Juliet Mills as Tabitha Lennox, a genuine witch whose daughter is named Endora and whose parents are a mortal named Darrin and a witch named Samantha. Furthermore, Bernard Fox has made two appearances on the show as his Bewitched character, Dr. Bombay.
The upcoming special Super Hero Wars: Kamen Rider vs. Super Sentai will be bringing together 240 heroes across both franchises, and once again Decade is involved.
The Friends episode "The One With Two Parts" introduces Phoebe's twin sister Ursula, who was a character on Mad About You. Both had been played by Lisa Kudrow, so it was an obvious choice (to the network, at least) to make the previously unrelated characters twins. That same episode had Jamie and Fran from Mad mistake Phoebe for Ursula.
One episode of Mad About You itself revealed that Paul's old apartment was being loaned to Kramer from Seinfeld.
And later it was revealed that the series Mad About You exists in the Seinfeld universe. Maybe it's a reality show?
Another Mad About You episode had Carl Reiner guest star as Alan Brady, his character from The Dick Van Dyke Show. This created a bit of a paradox, because in an episode of Friends (which would seem to be in the same "universe") the characters are shown watching ''The Dick Van Dyke Show."
Not as much as you might think: The actual DvD show ended with Rob Petrie trying to find a buyer for his life story, and Alan Brady hinting that he might want to turn it into a show, which is so meta it hurts. So, it's possible that, in the fictional world where Rob, Laura, and Alan Brady live or lived alongside the Mad and Friends characters, Alan Brady eventually settled on Dick Van Dyke to play Rob Petrie — brain exploding must stop...
Also, Chandler briefly appeared in a Caroline In The City episode, and Caroline briefly appeared in a Friends episode.
Ross appeared in an episode of The Single Guy, playing an old schoolmate of Jonathan's.
Daphne and Niles of Frasier were on an episode of Caroline In The City, too, so that links Frasier (and, by extension, Cheers) into this little sitcom world, too.
And since Cheers linked itself to St. Elsewhere, that drags all of 1990s Must See TV into the autistic kid's dream.
Some people Fan WankGreg House into the series as the passenger that tells Rachel off on her flight to England due to neither caring about the feelings of a nearby person and both being played by Hugh Laurie.
Martial Law also had a crossover with Walker, Texas Ranger. The first episode takes place on Martial Law and begins with the characters standing in their station discussing a recent crime. Then a voice rings out from off-screen, saying "I hear you could use some help." And then the camera shifts to a pair of cowboy boots and slowly pans up to reveal Ranger Cordell Walker, illuminated by a bare lightbulb overhead like some pagan godling. Then he and Sammo team up to stop violent, genocidal white supremacist militia members attempting to steal chemical weapons to use to ethnically cleanse Los Angeles. This is followed by an episode of Walker, Texas Ranger where Sammo visits Texas to help finish up the case. Sammo's extra-sensory and clairvoyant Chinese Daoist powers are accepted by the Rangers without a word of doubt. As Walker's long-suffering partner Trivette explains, "Around here, we call that sort of thing "Cherokee."
The Pretender had crossovers in paired episodes with The Profiler, and the relationship between the two characters was kept in the continuity.
Despite concepts seemingly custom-made for crossovers, JAG and NCIS only crossed over for one two-parter. Though NCIS didn't exist as a separate show when the crossover happened. In other words, a Poorly Disguised Pilot.
JAG's Lt. Bud Roberts did appear in the first season NCIS episode Hung Out to Dry.
Meanwhile, Lt. Cmdr. Faith Coleman and a Navy SEAL played by Adam Baldwin appeared on both series.
It's not quite Archie Meets The Punisher bizarre, but the special Alice two-parter that featured a visit from Boss Hogg, Roscoe and Enos from The Dukes of Hazzard (Boss Hogg was Not-Flo Joleene's cousin) is up there.
ITV drama series Footballers' Wives briefly exported popular character Tanya Turner to Bad Girls (also produced by ITV) when Tanya was jailed during the plot.
The creators of LOST and Heroes have discussed the possibility of intertwining their shows, but are largely unable to do so because they are on different networks. However, small details have crossed over. Characters on both shows have sported identical brochures for the fictitious Gannon Car Rentals.
Lost has also featured a few shoutouts to Alias, though it's unlikely they exist in the same universe due to Terry O'Quinn's characters in both shows being completely unrelated.
Actually, they do exist in the same universe, as a CIA agent is shown listening to one-hit wonderDrive Shaft, "You All Everybody", on his workstation. Ergo, Charlie Pace (played by Dominic Monaghan) is part of the Aliasverse, meaning LOST is part of it as well.
Likewise, an Oceanic Airlines flight to Sydney was mentioned in passing on Alias.
An Oceanic Airlines ad also appeared during the pilot episode of Flash Forward.
This could be because Oceanic Airlines is a generic name that a lot of shows use. The Other Wiki has details.
Also, the big "cork" on the bottle of evil at the end of the show pretty closely resembles a Hellmouth. Probably not intentional, but wouldn't it explain everything?
Speaking of LOST, one of Chef Robert Irvine's missions on Dinner Impossible was to cook for the cast of LOST. Though it was clear to everyone that LOST is only a television show, Nestor Carbonell did appear in character as Richard Alpert and Robert was given several Dharma food drops to work with, so it qualifies somewhat for this trope.
In an episode of Reba involving a court, the judge is obviously intended to be Philip Banks from The Fresh Prince of Bel-Air, and is played by the same actor, despite Reba taking place in Houston and Fresh Prince taking place in California.
Crossing Jordan and Las Vegas crossed over so often that it probably doesn't even qualify as intercontinuity crossover. They certainly take place far enough apart geographically that it's plausible that they're within the same continuity. I think that the Crossing Jordan characters made one more appearance in Las Vegas after their own show had been canceled, though both shows are now finished.
In one LV episode, Mary made a reference to booking a conference room for Dunder-Mifflin, and Heroes and the 2008 Knight Rider series have both made references. Linderman being involved would certainly explain the Montecito's high owner turnover rate. Don't combine it with the LOST bit above, though, or your head might explode.
When a mentally ill patient filed a paternity suit against Dr. Kiley on Marcus Welby, M.D., the trial was resolved by Owen Marshall: Counselor at Law.
Picket Fences crossed over into Chicago Hope (both shows created/executive produced/written by David E. Kelly and airing on CBS), when Fyvish Finkel's character Douglas Wambaugh checked into the hospital. They also poked at ER featuring a "commercial" for the hospital that parodied the opening credits of ER and later having one character say, "We don't like to talk about that other hospital."
Because both series were produced by William Dozier, it was practically foreordained that The Green Hornet and Kato would make an appearance in Batman, which they did in the episodes "A Piece of the Action"/"Batman's Satisfaction", which aired on March 1 and 2, 1967, as well as an appearance in a brief "window gag" in another episode. The styles of the two shows didn't really mesh, however.
As for the styles of the shows not meshing, in the Hornet's "window gag" appearance (the earlier of the two appearances), Batman and Robin acknowledge his and Kato's status as heroes. In the later guest appearance, the episodes run with the standard "on police records a wanted criminal" plot device of the Green Hornet property, and entangle the Hornet/Kato and Batman/Robin in a Let's You and Him Fight standoff.
The Mythbusters appear in an episode of the original CSI: Crime Scene Investigation (Vegas). From the way the segment is filmed its unclear whether they are intended to be fictional lab-techs, "themselves" visiting the lab, or a figment of Nick's imagination. However they later tested the same theory on Mythbusters, using clips from the CSI episode.
Speaking of CSI, that show once shared a rather odd crossover with the sitcom (and fellow CBS hit series) Two and a Half Men.
The franchise also crossed over with Cold Case and Without a Trace one time each. Some consider those two plus the three CSI series to be one big 'verse.
Fringe has a particularly interesting example of this trope. The Observer, or rather one of them, specifically September, whose task it is to police inter-dimensional travel and interferences with the timeline, has managed to crossover from the Fringe continuity... into the "real world". He appeared in the audience of American Idol and has been spotted in various stadiums during Fox sports broadcasts.
This one's a little older, but in an episode of The Jack Benny Program, Jack goes to court for supposedly murdering a rooster he owns. Who does he get as his lawyer? Perry Mason. Although it may not count officially, since it was All Just a Dream on Jack's part. Oh, and the true murderer? Perry Mason himself.
Ally McBeal and The Practice had a two-part crossover special that started on Ally McBeal on Fox and was resolved in the next hour on The Practice on ABC, with several characters from each show appearing on the other show. Both shows were produced by David E. Kelley.
1997's PrimeCracker, in which Fitz and DCI Tennyson hook up and decide that now they have a relationship they don't care who the killer is.
1997 also had BallykissDibley, in which Geraldine desperately tried to convince a visiting Father Peter that her parishioners were normal.
2009's When Janet Met Michelle, which combined all BBC Three's sitcoms about twentysomethings, as the cast of Two Pints of Lager and a Packet of Crisps invited characters from Grownups and Coming of Age to their fundraiser party. The title refers to the characters played by Sheridan Smith in Two Pints and Grownups, who did indeed meet.
In 2013, a skit with the 1950s midwives from Call the Midwife inexplicably in a modern maternity ward got even more bizarre when the increasingly exasperated father called for a doctor, and the TARDIS materialised.
Similarly, 2010's Children in Need telethon included EastStreet, in which a bunch of characters from each soap arrive at the location of the other one, including Gail Platt and Denise Johnson competing to see who has the most tragic backstory. The cliffhanger ending was that Liz Macdonald is Kat Moon's mother, in a direct parody of the revelation that Kat is Zoe's mother. See also the Doctor Who entry above for an earlier Children in Need'Stenders crossover.
Bryan Fuller likes to do this. Marianne Marie Beetle was a tenant of Jaye's trailer park in Wonderfalls, and then showed up at a competition in Pushing Daisies, despite the fact that Jaye's brother in Wonderfalls plays the main character, Ned, in Pushing Daisies, so they exist in the same universe, technically. And Jaye's mother is also Mother Superior in the second season of Pushing Daisies.
And Ned mentions the Happy Time Temp Agency by name, so Pushing Daisies and Dead Like Me exist in the same universe as Wonderfalls, which makes the Celebrity Paradox even more fun, because Jewel Staite plays a to-be-reaped record store employee in Dead Like Me, and then later played Jay's boyfriend's ex-wife in Wonderfalls.
Now Hannibal is part of the continuity. Gretchen Speck (she dropped the Horowitz in the divorce, apparently), from Wonderfalls, is in Hannibal, and played by the same actress. (And in Bryan Fuller fashion, Celebrity Paradox kicks in, because Caroline Dhavernas is in both.)
Niecy and Hakeem from Moesha appeared together in an episode of Clueless after UPN picked up that series.
This became a trend when Niecy appeared on Girlfriends and Maya appeared on Moesha as the aunt of Dorian's stepsiblings.
The character Peaches from Girlfriends made an appearance on Eve. Taking all the connecting shows into account, Brandy has masqueraded as no less than four people in the UPN-verse: Moesha, herself, Chardonnay (The Game, spinoff of Girlfriends), and a mystery caller on Sabrina, the Teenage Witch (which crossed over with Clueless).
New Japan Pro Wrestling has Jushin Liger, Tiger Mask, and Black Tiger, all of whom were anime characters before NJPW licensed their likenesses and created wrestlers out of them. It makes sense for Tiger Mask and Black Tiger, as the anime they originate from was about wrestling in the first place, but Jushin Liger was created for a Henshin series that takes place Twenty Minutes into the Future about a holy warrior with the power of the liger (half-lion, half-tiger) who battles evil aliens bent on destroying the world. Makes sense.
When Hulk Hogan's first movie, No Holds Barred, hit theaters, the WWF thought it'd be a good idea to bring in the villain of the film, Zeus, to battle Hulk in a WWF ring. They were never really clear on whether this was supposed to be the movie character come to life, or the actor assuming the character's persona to wreak havoc (in some promos, he'd lean one way, in others, the other), but one thing was absolutely clear throughout the entire angle: it was Wrestle Crap.
RoboCop (yes, RoboCop!) appeared at WCW's Capital Combat 1990 to rescue Sting from a cage he was placed in by the Four Horsemen.
Planescape, along with Spelljammer had partly come to be to facilitate crossovers by connecting the various campaign settings — or, to put it another way, to render Die, Vecna, Die style campaign-setting crossovers into ordinary crossovers. On the other hand, Ravenloft was supposed to have a rather one-way connection to the rest of the multiverse (things could enter, but they couldn't leave), so something coming out of Ravenloft to have a crossover was rather unexpected...
Paranoia had one of these with Cyberpunk in 1989 with the adventure Alice Through the Mirrorshades. In true Paranoia fashion, every aspect of Cyberpunk was given a thorough mocking, from its gritty near-future setting to it's "style over substance" ethos to creator Mike Pondsmith himself.
G.I.Joe's original intercontinuity crossover character, WWF wrestler Sgt Slaughter.
Hasbro has also done G.I. Joe action figures for Rocky Balboa and William "The Refrigerator" Perry as team trainers.
And also G.I. Joe action figures for Street Fighter II. In fact, it was there when Ken got his last name, Masters, because they couldn't name an action figure "Ken" thanks to Barbie.
For a few years, Hasbro had a Transformers sub-line called Transformers Crossovers, including Star Wars and Marvel Comics characters. They are presented as the characters driving vehicles that transform into Humongous Mecha that look like they do, ranging from a Hulkbot turning into a tank to a moon-sized Darth Vader robot transforming to the Death Star. The Star Wars ones have an advantage in that they can use existing vehicles to turn into. The Marvel ones don't have existing vehicles (for the most part... but then again, try remembering the last time you saw Spider-Man's Spider-Mobile), but this is an advantage in its own way as they can be designed almost entirely around making the robot mode look right.
There's also the Disney Label ones, including "Mickey Prime" and a Bumblebee Donald Duck. Doesn't seem like these Disney crossovers will be coming to the US, though.
Super Smash Bros. which features all of the first- and second-party Nintendo characters meeting (though technically it's not them, they're just Gashapon figurines brought to life). From Mario, to Link, to the Pokemon. And now there's the ones not from Nintendo, such as Sonic and Snake. AlsoMega Man.
Two games by Shounen Jump were made that put up some of their high-end mascots up against each other in the same vein as Super Smash Bros. The most popular and most varied is the Jump Super Stars game on the Nintendo DS. On the Gamecube, focusing on its most successful series, is Battle Stadium DON, with DON being an acronym for Dragon Ball, One Piece, and Naruto.
Wario Blast: Featuring Bomberman! which is what the title says. (Except in Japan, where it was GB Bomberman and had nothing to do with Wario.)
The Gilliam Yaeger who is the final boss of the Super Famicom game Hero Senki, and who appears in the Super Robot Wars initial continuity, and the Original Generation continuity are all the same character.
For that matters, the Super Robot Wars series itself is built on the idea of Mazinger Z and Shinji Ikari teaming up to beat up Char Aznable.
Also notable in Super Robot Wars OG Saga: Endless Frontier, Reji and Xiaomu from Namco × Capcom confirm that KOS-MOS from Xenosaga comes from their future (which was already established in the former's game).
Though it's technically one series, each of the Final Fantasy games has its own world and continuity, which means Gilgamesh's appearances in various games (it's hinted he's the same character, moving through the alternate universes) count.
The sidequest to get Cloud in your party. The PSP port of Tactics also included Balthier from Final Fantasy XII and Luso from Final Fantasy Tactics A2. In the case of Cloud too, it's suggested that his stint in Ivalice occurs when he fell into the lifestream, hinting that it's the actual Cloud from Final Fantasy VII. Less so with Balthier and Luso, who are more or less there with no explanation. Lampshaded by Balthier himself even, who mentions that his role in the game... "feels more like a cameo role".
DJ Atomica, the (some would say) annoying announcer in Burnout Paradise, is the same guy who provided the commentary for SSX 3. In Paradise, he makes reference to SSX several times, suggesting it's supposed to be the same character.
A couple of recent Yes! Pretty Cure 5GoGo! video games have incorporated characters from the previousuniverses. The story implications of the iDOLM@STER knockoff are probably not significant, but the DS game has a plot suggesting they all share a universe and simply never ran into each other before (which does happen in the Pretty Cure All Stars DX movie).
Some Ace Combat forum goers have taken the existence of iDOLM@STER skins in DLC to suggest that those characters are animated versions of actual musical artists in Strangereal.
Shin Megami Tensei III: Nocturne features a guest appearance by Dante from Devil May Cry. In exchange for this being done, series demon artist Kazuma Kaneko designed the Devil Trigger forms of the Sons of Sparda in Devil May Cry 3.
One of the boons from finishing an Escape Velocity: Nova storyline is access to one of two known (very expensive) ships "found floating near a wormhole at the farthest end of known space". Scientists "theorize that these mystery ships somehow entered our galaxy from a parallel dimension." The ship is from the original Escape Velocity game, which has practically identical (albeit less developed) gameplay but a completely different universe.
One of the earliest intercompany video game crossovers was Battletoads & Double Dragon: The Ultimate Team, a crossover between Rare's Battletoads and Technos Japan's Double Dragon franchises (natch) released in 1993 for various platforms. This was made possible by the fact that Tradewest published both series in America and Europe, although the game itself was really more of a Battletoads game with Double Dragon characters as guest stars ( some which were misnamed in the game).
"Disney" seems a bit unspecific, but that's because it's pretty much everything Disney owns.
As of Dream Drop Distance, characters from The World Ends with You are showing up, so now it's "anything Disney and potentially anything Square-Enix owns".
My World My Way features two characters, the mysterious dungeon diggers Owen and Kate, who were the protagonists of a previous Atlus/Global A game entitled Master of the Monster Lair. Owen even carries around the magic shovel that he had in Monster Lair, and the dungeon layouts are similar in both games.
Although it's all from the same company, this schtick is a favorite of Nippon Ichi. Characters tend to show up in each other's games with reckless abandon, ranging from minor cameos to secret characters to actual plot-relevance. Laharl ends up in a bottle in Phantom Brave and chews out Revya in Soul Nomad & the World Eaters for trying to take his title. Etna is a central secondary character in Disgaea 2. Lujei (from Grim Grimoire) is responsible for Endorph (who is really Walnut from Phantom Brave) appearing in Soul Nomad. Everyone of any importance shows up in Disgaea 3 as downloadable content. And to top it off, you have Asagi, the wandering protagonist without a game of her own, trying to usurp the hero role in almost every game.
Interesting crossover here, in Devil May Cry. Dante receives the sword named Alastor, imbued with an electrical motif. Later on in Viewtiful Joe, a character named Alastor appears, complete with the electrical motif. The connection is later made in the PS2 port of Viewtiful Joe in which Dante guest stars and Alastor (revealed to be the spirit of Dante's sword) harbors some unfriendly feelings towards Dante (for leaving him behind in Devil May Cry 2).
After this, the connection is pushed forward in Tatsunoko vs. Capcom in which Morrigan's win quote vs. Viewtiful Joe mentions that she was disappointed in him after talking to Alastor. Leading to an implication that Darkstalkers, Devil May Cry, and Viewtiful Joe are all part of the same universe.
Done again in Marvel vs. Capcom 3, where Dante and Joe's unique intro quotes for each other show the two to be friendly acquaintances. This would be odd, as Dante never actually ran into Joe in his Viewtiful Joe story, but he was playable in the PSP version of Viewtiful Joe: Red Hot Rumble.
Bayonetta, another Shinji Mikami creation, drops numerous hints that it exists in the same world as Devil May Cry. This is particularly done through the use of Enzo, who has the same name and personality traits of an information broker who was pals with Dante and mentioned as early as the instruction manual for Devil May Cry, but the lore for one of the unlockable accessories, the Bracelet of Time (which is visually similar and functionally identical to the Bangle of Time from DMC1), notes that it was created by Eva (Dante's Missing Mom), "a truly extraordinary [Umbra] witch" who "entered into contract with a legendary dark knight" (i.e. her husband Sparda). Additionally, Luka's father is a world-famous journalist well versed in the supernatural who goes by the name Antonio Redgrave. Dante's preferred alias in the DMC1 novel and The Animated Series? Tony Redgrave. When asked about the connection, Kamiya answered on his Twitter account that Dante respected Antonio and his work, so took the name during his early days as a demon hunter. Luka also name drops Claire, Trish, Silvia, and Ammy as girls he's dated in the past, but that's presumably a fun little nod to Kamiya's past works.
Metal Gear Solid 3: Snake Eater featured a bonus minigame where Solid Snake is assigned capture a bunch of escaped monkeys from the Ape Escape series. In turn, Ape Escape 3 featured a bonus mini-game where the player controls a monkey named Pipo Snake who must rescue Solid Snake.
Via "Fall of the Space Core, Volume 1", a mod collaboration for The Elder Scrolls V: Skyrim between Valve and Bethesda, the Space Core from Portal 2 crash-lands near Whiterun and gets picked up by the Dovahkiin. No word on where Wheatley ended up.
Or as Valve put it, a patch to put Nolan North in Skyrim.
Reality On The Norm, a Shared UniverseRound Robin series, has had some games about character from other games entering the city of Reality, such as Commander Keen or Monty Mole. Then there's Shadows of RON, whose developer actually included the character from his own book series as the protagonist.
Unwinder of Unwinders Tall Comics adopted Marmaduke. Then, in the Watchmen parody comic, the big dog dies à la Jon Osterman. According to the author, "It's not Tall Comics canon, but it IS Marmaduke canon."
In a guest strip for PvP, Kris Straub proposed that his comic Starslip takes place in the same universe, just thousands of years later, and his characters are descendants of those in PvP. Scott Kurtz said it's canon, though maybe he was joking.
Cross Time Cafe: Characters from at least five different webcomics are regular cast members - though half the cast appears more here than in their own comics (the main exceptions being Florence, Jack and Jenny.
I'm a Marvel... And I'm a DC has Marvel and DC characters (and occasionally characters from other continuities, such as Hellboy) arguing with each other about whose comics and movies are best. Then there's the "After Hours" series which has actual storylines involving characters from both continuities, in the same vein as the official Marvel/DC crossovers.
There was a competition between most of the major Fantasy series - based on popular opinion, not on what makes any sense. For example, The Dragon Reborn, Harry Dresden, Kovthe all lost to muggles. Each one had a written description of the battle - and despite the implausibility, it was awesome.
Transformers and G.I. Joe have a long history of crossovers, which includes Inhumanoids and Jem through the shared character of sensationalist TV reporter Hector Ramirez (a Geraldo Rivera parody). The original comic books had a special crossover miniseries, and recent comics have revisited the crossover in various ways. The old eighties cartoons, meanwhile, shared a reality: in the futuristic third season of Transformers, major character Marissa Faireborn was the daughter of G.I. Joe character Flint, and one episode featured a washed-up Cobra Commander doing business under the pseudonym "Old Snake."
Disney took this to another extreme with Lilo & Stitch: The Series, doing several specials that crossed it over with a bunch of the other shows on Disney Channel. This fits with the movie's initial marketing push, showing Stitch crossing over with various Disney movies, wrecking the place, and being told to get his own movie.
And, as a result, aliens are now canon in Recess and The Proud Family... Which seems kinda odd, considering how relatively realistic their premises were. Though it does somewhat fit with The Proud Family's usual weirdness. Penny's great-aunt canonically has telekinetic powers.
It's very confusing with Recess, as it's made explicitly clear in the series that it takes place over the course of the Fall of 1997 until the Summer of 1998 (and then Fall 1998 for Recess: Taking the Fifth Grade), even for the episodes made in the 2000s (this is firmly established in Recess: School's Out)
Made even worse when you realize that Lilo and Stitch were originally from the Disney Animated Canon, which means that all of the Disney Channel cartoons take place in the same universe as all of the Disney animated features... EEK!
In one episode of Duck Dodgers, Dodgers gets his dry cleaning mixed up with Hal Jordan's and ends up as the newest Green Lantern when he finds the power ring in Jordan's uniform pocket.
The episode name, for the curious, is The Green Loontern. And in another episode (Samurai Quack) Dodgers takes the place of Samurai Jack. Complete with Achoo, voiced by Mako himself.
In a move which infamously pissed off Groening, Jay Sherman from The Critic comes to help judge a film festival. An episode made after The Critic was canceled has Jay turn up again, this time confined to an insane asylum and only able to say his Catch Phrase, "It stinks!"
He appears again, along with other one-time characters voiced by Jon Lovitz.
There were also plans to do a crossover when it seemed there would be a series version of Atlantis The Lost Empire, called Team Atlantis. Set in the '20's, it would have involved the Atlantis cast getting involved in a battle between Demona and a former Hunter.
However, that hunter has reappeared in the comics, and Demona was seen grabbing something out of the remains of the Praying Gargoyle an Atlantean crystal.
The Mask and Ace Ventura met for two episodes that could have been awesome. Both shows kept their respective styles of animation in each other's universe (Ace & Spike, for example, kept their more cartoony look in the Mask's more realistic world and vice versa).