The X-Men movies and comics do these gags toward each other:
In the first movie, Logan isn't thrilled by his black leather X-Men costume. Cyclops taunts him, asking if he'd prefer yellow spandex — Wolverine's traditional costume in the comics.
The comics Rogue has a poster of The Piano (in which Anna Paquin, movie-Rogue, appeared.) and Nightcrawler puts down Brainchild's fake English accent (as Scottish actor Alan Cumming was put down for the fake German accent he used with movie Nightcrawler.)
In an issue of Uncanny X-Men, Wolverine and Storm go to see the Broadway production of Seven Brides for Seven Brothers. Wolverine comments that the lead actor reminds him of himself; it was Hugh Jackman.
Additionally, in an issue of X-Treme X-Men, Storm is at one point complimented on a recent James Bond movie, having evidently been mistaken for Halle Berry, who played both Storm in the X-Men movies and Jinx in the then most recent James Bond film, Die Another Day.
X2: X-Men United has a line from Magneto: "When will these people learn how to fly?" which, according to the screenwriters, was supposed to be a subtle Take That, Us at the movieverse Rogue and Storm (and to a lesser extent, Jean), who of course can fly in the comics.
A comic-to-comic Mythology Gag: For those who remember the original Phoenix Saga, in which the alien Shi'ar Empire sentence Jean Grey to death (not to mention the recent story where they wipe out her entire family, just to be on the safe side), there's something very ironic about Ultimate Marvel's human "Church of Shi'ar Enlightenment" funding the X-Men because they want Jean to manifest the Phoenix. All the same players (more or less), very different game.
In an issue of X-Men, shortly after the Grey massacre by the Shi'ar Death Commandos, Scott enters Rachel's room and finds several rented movies on her bed. The films all star cast members of the X-Men film series, such as Swordfish, which featured Halle Berry and Hugh Jackman, who played Storm and Wolverine in the X-Men trilogy, respectively.
There was an issue where Beast says, "In the words of my favorite TV psychiatrist, I'm listening." Dr. Frasier Crane's catch phrase, played by Kelsey Grammer, who also played Beast in the movies.
In the standard BatmanBack Story, Bruce Wayne is inspired by a bat that flies in through an open window while he's trying to come up with a motif that will strike fear into the hearts of evil-doers. In The Movie of Batman: The Animated Series, a Flash Back to the early days of Wayne's crimefighting career shows him trying to come up with a motif that will strike fear into the hearts of evil-doers... but it's raining, and all the windows are closed. (He eventually does have the bat inspiration, but later and under different circumstances.)
In the movie, the bat can be briefly seen before flying away.
Similarly, in The Batman vs. Dracula, he has a nightmare that starts with the window closed, and the bat crashes through it and dies.
The bat crashing through the window is canon in modern continuity (or at least it was): The bat was deafened by a scientific experiment done by Kirk Langstrom, who would become Man-Bat. Seriously.
In the ElseworldDetective No. 27, in which Bruce Wayne becomes the World's Greatest Detective without donning a costume, he is interrupted in his revery by the arrival of Lee Travis (the Crimson Avenger) inviting him to join the Secret Society of Detectives. So he shuts the window and leaves the study, and doesn't even look round when something "thunk"s against it.
Heck, the title itself is a Mythology Gag. Tell me, what comic and issue number does Batman debut in?
Similarly, in In Darkest Knight (where Bruce becomes Green Lantern instead), the bat is scared off by a projection of Abin Sur, who crashed on Bruce's property.
The TV and movie adaptations of DC's Superman/Superboy characters have provided a rich treasure trove for fans of the Mythology Gag.
In Richard Donner's Superman (1978), there is a scene where Clark desperately needs to become Superman. He runs to the nearest pay phone, then stops — apparently expecting an old-style phone booth and ending up with a then-new phone-on-a-post instead.
That joke was foreshadowed in the 1975 inter-company crossover Superman vs. the Amazing Spider-Man, only there it happened to Spider-Man.
It also recreates on film an iconic image from the cover of the first issue of Action Comics, which featured Superman dashing the front end of a car into the ground — albeit that the film version inverts it as part of Superman's successfully lowering the out-of-control car to the ground. The image even reappears as a photograph of Superman later on in the film.
It gave a (parodic) nod to a Catch Phrase from the early Superman radio serials and later Silver Age comics ("Look! Up in the sky! It's a bird! It's a plane! It's Superman!"): Lois Lane, Perry White, and Jimmy Olsen are looking over some blurry photographs of something flying in the skies over Metropolis. Lane says the shape is a bird. White disagrees and says it's a plane. Jimmy Olsen begins to say "It's—" but is cut off by a knock on the door as Clark Kent enters, saying to White "You wanted to see me?"
The original Superman movie also subtly parodies the Catch Phrase. As Superman flies through the air in his first public appearance to rescue Lois Lane, a couple of reporters with a camera remark on camera "What the hell's that?"
There's also a scene where Superman utters the line "Well, I hope this experience hasn't put you off flying. Statistically speaking, it's still the safest way to travel." In the first movie, it's said to Lois. In Returns, it's said to the plane full of passengers that Supes has just saved.
Also in the movie, Superman's first heroic deed upon returning is saving a space shuttle. In the comics, his first Post-Crisis appearance was also saving a spaceplane.
Not to mention the entire plot being Superman foiling a real estate scheme by Lex Luthor that will kill millions.
Going the other way, JLA: Earth-2 had the League burst into LexCorp, and Luthor say into his intercom "Miss Tessmacher, hold my calls." Not a Canon Immigrant, because she doesn't actually appear, but...
During his time as President Evil, Luthor also had a bumbling PA called Nathaniel "Mac" Mackelveny, who was clearly modeled on Otis from The Motion Picture right down to calling him "Mr Lew-thor". He was eventually revealed to be the Martian Manhunter.
In the Forever Evil tie in Action Comics #23.3 / Lex Luthor #1, much is made in the first few pages of Lex's loathing for his prison jumpsuit, which he states he never intends to wear again, and has burnt because there's nothing about that he wants to remember. This is a reversal of the Silver Age Luthor's reaction to Superman sending him to prison, which was that he would always wear the uniform to remind himself how much he hated Superman.
The late 1980s-early 1990s NOW Comics adaptations of The Green Hornet featured a number of Mythology Gags referring to both The Green Hornet and The Lone Ranger (another property created by the creator of The Green Hornet). In the entire series (an ambitious reconciliation of the Hornets of the radio series, 1940s film serials, and the TV series), the second Kato (partner of the TV series Hornet) is named "Hayashi Kato", a reference to actor Raymond Hayashi, the first actor to play Kato in the radio series. In the comic book Green Hornet: Dark Tomorrow, the Green Hornet of the future is named Clayton Reid. This is a reference to the actor Clayton Moore, best known for playing the Lone Ranger, who is often claimed as the Hornet's ancestor. Also, a family tree feature giving the genealogies of the Reid and Kato families gave Clayton Reid's father the name "Gordon Reid" (a nod to actor Gordon Jones, who played Britt Reid/The Green Hornet in the 1940 film serial) and stated that a future Kato would be named "Luke" (a nod to actor Keye Luke, who played Kato in both the 1940 and 1941 film serials).
Also, Rohjaz/Captain America is referred to as "the Forerunner", and is basically the universe's trigger to kick off the age of superheroes; the character in question was one of Marvel's first superheroes, predating most of the other characters' publications by two decades.
Lex Luthor's plan appears to be, when he first reveals it, exactly what Grodd planned for the New Secret Society / Legion of Doom in Justice League, a protection racket for supervillains (he eventually reveals that it is something else). Later on, Grodd and Luthor have a conversation where Luthor gives orders and Grodd begrudgingly relents, apparently planning to overthrow Luthor, a reversal of the Justice League relationship.
Yet another "Legion" example: Most of the characters in the Dark AgeSpace Police comic L.E.G.I.O.N. were callbacks (or callforwards?) to characters from Legion of Super-Heroes: Vril Dox and Lyrissa Mallor were distant ancestors of Brainiac 5 and Shadow Lass; Lar Gand and Phase were time-displaced versions of Mon-El and Phantom Girl; Strata, the Durlan, and Dagon-Ra were the same species as Blok, Chameleon Boy, and Element Lad; and so on.
The 2009 R.E.B.E.L.S. series continues this, with Dox's new recruits including Wildstar, who comes from the same planet as Dawnstar and combines Dawny's powers and name with those of her love interest Wildfire; and Bounder, who wears an inflatable armoured suit that duplicates Bouncing Boy's powers.
And given that it wasn't even an especially memorable story, it's amazing how many ways Post-Crisis continuity found to refer to Superman getting a big, red ant-head. In one case, a squad of "Super-Ants" were created by an insectoid alien who based her human form on Lana Lang, another Mythology Gag, because pre-Crisis Lana was an occasional super-heroine called Insect Queen.
In #12 of the New 52Action Comics, Superman is given a vision of a "perfect world", which is basically the pre-Flashpoint universe: his parents are still alive; he started working at the Planet with Jimmy and Lois from his first day in Metropolis; the League headquarters is a moonbase; and he's married to Lois. That last one is when he realises this doesn't make sense.
One memorable Running Gag is in Ultimate Spider-Man: whenever Spidey swings by the police station, the cops are taking away some screaming nut in a superhero costume who somehow references the latest Crisis Crossover in the main Marvel universe. So far we've seen "Scarlet Witch" claiming that she wasn't crazy (House of M), "Speedball" yelling "Not like this! Not like this!" (Civil War), and "Elektra"(?) asking who can you trust (Secret Invasion).
We've also seen a female dressed suspiciously like a Green Lantern shouting, "Choose your side!! Choose your side!!", suggesting the comic has progressed to needling the Distinguished Competition (Green LanternCorps and its storyline Blackest Night).
A girl dressed as Spider-Woman was seen during a story which marked Ultimate Mysterio's debut.
After his Opposite-Sex Clone leaves, Peter muses on her organic web shooters before dismissing them as a silly idea. During this time, the main Marvel Universe Spider-Man still had organic web shooters.
At one point in Ultimate Spider-Man, Sam Raimi is directing a Spider-Man movie starring Tobey Maguire with (judging from Spidey's "You were cool in Evil Dead" comment) Bruce Campbell involved somehow. Why does that sound familiar?
Ultimate Beetle (who has an entirely different origin from 616's Abner Jenkins) wears an armoured suit that looks a little like the classic Beetle, and a lot more like Jenkins's later identity of M.A.C.H.-V.
Deadpool, notable breaker of the fourth wall, once commented, "And the Boy Scout branch made a big show of cooperating, by having Spider-Man reveal his identity on national TV... as if we hadn't seen the movies already and didn't know it was dreamy doe-eyed Tobey Maguire under the mask!" Maguire, of course, played Spider-Man in the movies.
It should be noted that Deadpool does things like this frequently. In the third issue of his own series, he sings the theme song from the 1960s Hulk cartoon.
When he was being controlled by the Hypno Hustler in Avenging Spider-Man, the trigger word to free Deadpool from his trance was "Ryan Reynolds." Reynolds portrayed Deadpool in X-Men Origins and was supposedly casted as him for the long rumored Deadpool solo movie.
In the first issue of Greg Rucka's Queen And Country, SIS agent Tara Chace comments, "the last time I was this cold, I was in Antarctica," which is a nod to Lily Sharpe, the SIS agent in the writer's first comic, Whiteout. Rucka originally intended to use Sharpe as the lead for Q&C, but in the course of development, Chace became more of a Spiritual Successor.
Also, The Movie has something of a cross between this and a Discontinuity Nod in the codename of Ozymandias's movie-changed plan, seen on a computer in one scene. The name? S.Q.U.I.D. — which refers to the fan nickname for the comic's original method.
Kevin Smith's Batman: The Widening Gyre opens with a Flash Back to the days when Dick Grayson was Robin, as they try to stop a Neo-Nazi supervillain stealing an ancient copy of the Torah. Robin makes his entrance shouting "Holy scrolls, Batman!"
Being a time traveling superhero, this comes with the territory for Booster Gold, as he makes references to events and people in The DCU during his heroics through time. For instance, in an effort to keep Sinestro from meeting Guy Gardner early, Booster inspired the naming of the Sinestro Corps.
ElfQuest — the second series titled Wavedancers features one insane and deformed character whose delusions apparently are based on the first Wavedancers series, which was removed from the canon because of differences with the team that made that.
In one Marvel What If? story, Logan is an Expy of The Punisher and takes on the Chicago mob in the Roaring Twenties. He never pops his signature claws, but when we get to see Al "Scarface" Capone from the front, the mob boss has a scar suspiciously reminiscent of the wounds that 616-Wolverine would cause.
In a Marvel UK Transformers Generation 1 comic, Optimus Prime mentions that Swoop was known as Divebomb on Cybertron. When the toys were originally being released, Divebomb was considered as a name for the toy that ended up being named Swoop.
In a movie tie-in comic, Optimus has been recently found out to be a Prime. He makes a comment saying it might not be important, comenting along the line of "For all we know, Prime could mean 'records clerk' or something." In the Dreamwave comics Optimus was a records clerk before he became Prime.
In one Dreamwave comic Megatron basically beats the ever living slag out of and kills Cy-Kill the Gobot (not sure if that's a mythology gag or a shout out though).
At the end of the IDW Transformers storyarc All Hail Megatron, as the defeated Deceptions flee into space, Starscream ponders on what to do with the badly injured, near dead Megatron, saying at one point "I'd unceremoniously toss him out the air lock if I didn't have a nagging suspicion that he'd somehow return, more powerful than ever." This is exactly what Starscream did in the original animated movie, which ended with Megatron becoming the more powerful Galvatron and returning to kill Starscream in revenge.
Another reference to this occurred in a four part series set at the start of the Autobot-Decepticon War. Scorpionok betrayed Megatron and left him for dead in order to assume control of the Decepticons himself. Just as he was doing so, Megatron came storming in, complaining that it was "bad comedy." Scorpionok looked up to see the strange (Megatron had repaired himself using Junkion tech) 'Con standing at the end of the room.
Scorpionok: Megatron? Is that you?
Megatron: Here's a hint! (Shoots Scorpionok in the chest)
The Hack/Slash and Re-Animator crossover ends with Doctor West being approached by government agents, who tell him the president is dead and the country needs him, a nod to the unmade House of Re-Animator.
There's a subtle one in the introduction of the handheld supercomputer Nicole: In the cartoon, Sonic develops a bit of a habit of shaking her when the words she uses get too big for him. It's funny, but more than a little uncomfortable. In the comic, it's the first thing Sonic tries with her until she fights back by shocking him.
Sally: That wasn't very nice, Nicole!
Nicole:Neither was nearly shaking me to pieces!
The one-shot all-humor 1982 comic "The Fantastic Four Roast" does a little zig-zagging. When Dr. Doom takes the podium, he says that he became Dr. Doom after being upset that Reed Richards and his college brothers didn't invite him to go on a panty raid.
In Mega Man, the first issue's Short Circiuts had Mega Man asking if he was now a Super Fighting Robot. As it turns out, he was upgraded into the infamously bad cover art from the first Mega Man game.
Graphics Classics: HP Lovecraft: "Sweet Ermengarde" is a comedy rather than cosmic horror, but for this product, it was illustrated as a play put on by humans for an audience of Eldritch Abominations. The front row of the audience includes a Deep One, Herbert West (with a severed head and a syringe), Keziah Mason and Brown Jenkin, referencing The Shadow over Innsmouth, Herbert West, Reanimator and Dreams in the Witch House.
Which makes sense. If the destruction of the Kelvin didn't affect her up until then she likely was in the Academy at that point anyway.
The DC One Million 80-Page Giant included the first meeting of Superman 1M and Batman 1M, in which they both disguised themselves as villains to infiltrate a meeting of the Superman and Batman Revenge Squads. The meeting took place on an interdimensional freighter called the Varania, which also happens to be the name of the cruise ship where Clark and Bruce first learnt each others' identities in Pre Crisis continuity.
Kingdom of Monsters had the president ask what would happen if they dropped a nuke on Godzilla with the supposed consequence giving him laser eyes.
Battra coiling around the Eiffel Tower harkens back to Mothra.
The way Godzilla, Anguirus and Rodan are introduced are very much in line to how they were introduced in their respective movies.
Godzilla Legends, full-stop. Issue one, we have cameos by King Ghidorah and Gigan, issue three has the retro style MechaGodzillas and issue four has a cat seen in the sludge covered remains of a city and a quip about Godzilla flying.
Godzilla Gangsters and Goliaths: the fairies of Mothra are referred to briefly as the Shobijin, the Cosmos and finally, as they're called in the comic itself, the Elias.
Godzilla: The Half-Century War is chock full of these. In issue one, it's a P.O.V. Sequel of Godzilla 1954. There's also a building with a squid logo resembling Gezora. Issue 2, Anguirus doing his spike move from the Showa series (in that he turns around and launches himself backwards). Issue 3 has a guy named Dr. Deverich (it also counts as a Take That to Roland Emmerich and Dean Devlin). Issue 4 is a narrowed down Whole Plot Reference to the original script of Godzilla vs. SpaceGodzilla but with a container that was supposed to be used in Godzilla vs. MechaGodzilla II's original script. Issue 5 is a homage to Godzilla vs. Gigan and is set in Antarctica just like Final Wars, At World's End and Godzilla Raids Again.
In issue 11 of the ongoing Godzilla comic, Godzilla uses his breath ray to propel himself upward like a rocket to escape the ravine he gets trapped in during his battle against Hedorah.
In the Rulers of Earth series, just the very preview pages are full of MGs. Zilla's arrival is almost like the 1998 film and the Yahlen boat from Ebirah Horror Of The Deep, not to mention a cameo by Shockirus. There's also an appearance of the the Gotengo as a model, Godzilla's Japanese name and the fact Lucy's hotel room is called 1954, a not so subtle reference to the first film.
In the first issue of Roger Langridge's Popeye comic, when Castor Oyl asks Popeye if he'll help them "rustle up" a creature, Popeye quips "Rustle up? Ja t'ink I'm a cowboy?", a nod to his first line from the original Thimble Theater strip that introduced him.
During the "Zen and the Art of Gazebo Repair" arc, we see Pinkie Pie, Rainbow Dash, and Rarity relating an adventure involving giant bees and a Sun Stone, a nod to the My Little Pony And Friends arc "The End of Flutter Valley".
The DC Elseworlds story, Superman/Wonder Woman: Whom Gods Destroy, written by Chris Claremont, is set in a universe where Artemis and Athena transform Lois Lane into Wonder Woman, while turning Lana Lang into the Oracle of Delphi so that they may join with Superman in battle against Ares and his followers. The story ends with Lois, Lana and Superman in a polyamorous relationship. In real life, William Moulton Marston, the creator of Wonder Woman, had a deeply committed polyamorous relationship with his wife and another woman.
In Red Robin 19, Tim Drake, a former Robin, trapped in the Unternet, wakes up and wonders where he is, but then states, "Well that answers that", saying it's a nightmare. Next page reveals that he is looking at a Silver Age Batman and Robin fighting Silver Age bad guys to which Red Robin responds, "Holy make believe". This same statement also doubles as an answer to a riddle by the Riddler.
Batwing's costume looks a lot like the imaginary African-American Batman (aka "Bat-Wings") in the seventies comic "The Batman Nobody Knows". Only less seventies.
In the zero issue of IDW's Dungeons & Dragons comic, halfling rogue Bree attempts to pry the ruby from the left eyesocket of a familiar looking statue◊. (The gem in the right socket has already gone, of course.)
The fourth issue of IDW's The New Ghostbusters has a subtle nod to Louis Tully from the movies combined with a Shout-Out to Scooby-Doo when Egon says the group has to split up:
Ron Alexander: Do you guys also have a talking dog?
In SuperboyVolume Six Jon Lane Kent, the son of Superman and Lois from a possible future and template for Superboy, wears a costume that looks a lot like the 90s Superboy costume.
Adding on to that, Superboy's status as an opposite morality clone of another Superboy makes him the Nu52 version of Match. Jon Kent and the Post-Crisis Superboy were emotional and extroverted teenagers, while Match and Nu52 Superboy are their stoic and technically superior clones. Jon Kent was even mentioned as having genetic issues, a common problem for the first version of Kon-El.
In the Fantastic FourSpin-OffFF, the adult members of the Future Foundation include Darla Deering, a pop singer wearing the Thing-suit Reed invented one of the times Ben lost his powers. Later, Ant-Man improves it so she can summon the suit by touching two rings together - a reference to Benjy Grimm and his Thing Ring from the Fred and Barney Meet the Thing cartoon series.
Web of Spider-Man #75 includes multiple cameos as various heroes deal with the villain causing a snow storm in New York, but makes a point of having Spidey interact with Iceman and Firestar, as a reference to the animated series Spider-Man and His Amazing Friends.
In another issue where everyone holds a memorial for Peter Parker, Iceman has an Imagine Spot that references both Amazing Friends, and the then current Ultimate Spider-Man cartoon, featuring Spidey leading a team consisting of Firestar, Iceman, Nova and White Tiger.
The Beano dated 5th April 2014 includes a flashback to when Dennis's Gran was a little girl. Her dad (Dennis's great-granddad) looks just like Dennis's Dad did before the 2012 revamp of Dennis's parents.
In Batman 66 #3 (the comic based on the Batman TV series) there's a character called the Red Hood, who looks a lot like the original Red Hood from regular continuity (that is, The Joker before he became the Joker) and claims to be the Joker's greatest enemy. He turns out to be the Joker's psychiatrist, possessed by the Joker's subconscious through his brainwave helmet and acting out a plan to free him. In the same story, one of the other psychiatrists at the Arkham Institute is Dr Quinn, who refuses to call the Joker by his criminal name, and therefore refers to him as "Patient J".