In Mighty Avengers, Hank Pym has almost become a walking shout-out to the Doctor Who fandom. Multiple identities, personalities, and costumes over the years? Check. Female sidekick? Yep, Jocasta fits that right there. Heck he even has a do anything tool, i.e. Sonic Screwdriver, thanks to the use of a smart chip and Pym Particles to store multiple tools in one tiny thing. His base is even so similar to a TARDIS that Amadeus Cho calls him on it.
Avengers Assemble introduces the football-based British superheroine Magic Boots Mel, who is basically Jess Bharma with "Billy's Boots" from the Roy of the Rovers strip of the same name.
The Awesome Slapstick features several of these, to Marvel, DC, WB characters, and basically anything that the creators thought funny, especially in the second issue which took place in a mall.
In the Marvel comic Blaze of Glory: The Last Ride (essentially a "whatever happened to...?" focusing on Marvel's Wild West characters, specifically Two-Gun Kid, Rawhide Kid, Kid Colt, Outlaw Kid, Gunhawk, and others) a young boy excitedly rattling off the names of his dime-novel heroes mentions the name "Jeb Kent" - a character from the DC series The Kents (written by the same author).
Oh, and the large number of characters with "Kid" in their nickname is humorously lampshaded within that issue; someone runs into the bar where they are drinking and calls out "Hey, Kid!" and they all turn and say, "Yeah?"
In Captain America/Thor - The Mighty, Fighting Avengers, both Thor and Cap wind up in Camelot to discover Loki pretending to be Merlin. How does Loki explain away the change in appearance and demeanor to King Arthur?
Arthur: And you, Merlin... You seem now to have completely recovered from your... What did you call it...?
Made funnier by a comment in the new series that River Song hates wizards in stories because they always turn out to be him. (And indeed, the old series confirmed that he was indeed Merlin.)
Daredevil: In Daredevil (Mark Waid) Vol. 3 #10, Daredevil demands to know what The Moleman plans to do with a body he has stolen - asking if he has discovered a "Resurrection Bath" in his underground kingdom, a rather obvious nod to the Lazarus Pits of Batman fame.
In Deadpool 1997 #27, Deadpool address Kitty Pryde, "You smug little— Speaking of games. You ever play Street Fighter?◊" This is later referenced in an actual Street Fighter comic, where Ryu says "Speaking of comics, you ever read Deadpool?" before hitting Sagat with the very Shoryuken that gave him the scar on his chest.
Hitler: Here is where the Fourth Army should crush Sergeant Fury and his Howling Commandos from the flank. They have been a constant thorn in my side, but no longer! General: My Fuhrer... Another general: My Fuhrer... Sergeant Fury and his Howling Commandos have smashed your Fourth Army and continued their march towards Berlin. A third general: We don't know their current location. Hitler:[after shakily removing his glasses] Son of a bitch! What are they, like— Six men? I have millions of soldiers out looking for a bunch of drunken braggarts! How hard is it to kill Nick Fury? He wears an eyepatch!!! Just sneak up on him in his huge freaking blind spot!!! Then stab away! Ach. If these are my last days, don't tell anybody about them. I don't want any books or films to be made portraying me as the lunatic captain of a sinking ship.
Doctor Strange: In Doctor Strange: The Oath, Strange travels to another dimension to face "Otkid the Omnipotent" and retrieve an elixir which he hopes can cure his servant Wong's inoperable cancer. The Corrupt Corporate Executive trying to destroy this medicine (he runs a pharmaceutical company) has a copy of The Fountainhead on his desk. Both are references to Doctor Strange's creator, Steve Ditko.
Fantastic Four: Tintin managed to have a cameo in Fantastic Four (1998) #1, drawn by Scott Lobdell and Alan Davis where Reed and Sue (in disguise) meet the reporter during a protest march, where he is addressed as French, but quickly points out: "For the record, I'm Belgian.". Later in the story he is seen again fleeing, while shouting Haddock's catchphrase: "Billions of blistering blue barnacles". [1]
The Invaders: In Giant-Size Invaders #1, which details the teams's formation, a weakened Master Man is forced to flee from the heroes, resulting in a few shout-outs to Superman: The narration states how, now that his strength is leaving him, Master Man has no hope leaping through even a short building in any number of bounds, and Bucky states that he's still "faster than a speeding bull-dozer".
Edwin Jarvis, butler to Iron Man and The Avengers, is named after Alfred Pennyworth's father Jarvis, mentioned when Alfred first appears in Batman #16 (1943).
In Kieron Gillen's Iron Man 2012 run, a former mentor of Tony's named Eli Warren is introduced. In case the name is too subtle, he also looks and talks just like Warren Ellis.
Loki: Loki: Agent of Asgard has the mysterious arc words "That which is called ego-death is coming for you," which is a quote from, of all things, Timothy Leary's The Psychedelic Experience.
In Marvel 1602: Fantastick Four, the counterpart of Namor/the Sub-Mariner is named Numenor, and his (unsunken) country is called Bensaylum, after Bensalem in Francis Bacon's The New Atlantis.
In Marvel Universe #8, and subsequent stories, Mole Man is given the real name Harvey Elder. This is a reference to Harvey Kurtzman and Will Elder, creators of the criminal "Melvin Mole" in MAD #2. (This then gets referenced slightly differently in the Spider-Man newspaper strip, where his name's Melvin Kurtzman.)
In the 90's Morbius comic, a nurse asks "Who's Darkman?" when she sees Morbius covered by bandages when he's escorted to a hospital while trying to keep his identity a secret.
Bruno's co-worker at the convenience store is named "Chatty Bob."
There is a brand of hot sauce in Bruno's convenience store called "Dylan's Hot Fiyah."
Magical Pony Adventures is Earth-616's counterpart of our My Little Pony (Generation 4), complete with names such as "Rainbow Toots".
When trying to research her new powers, Kamala kept finding web-pages dedicated to World of Battlecraft instead of anything helpful when searching for "Polymorph"note there is a spell by that name in 'World of Warcraft''.
During Kamala's rant to Kaboom about how her people (Muslims) suffered for the actions of a dangerous few and how Inhumans will suffer for her's, she yells "Not again! NEVER again!". This references the well-known rallying cry for victims of the Holocaust and other ethnically-motivated genocides, which would later be appropriated as a slogan for the Jewish Defense League.
The Snarks, enemies to Marvel Comics' Power Pack, were a Shout Out to Lewis Carroll; in-story, they were so nicknamed by another alien with a fondness for Earth literature.
In perhaps the most esoteric reference, during the "Dead End Kids" arc, the team walks past a woman who looks a hell of a lot like the early feminist Emma Goldman.
During the first Morlun arc (by J. Michael Straczynski), a couple of workers at a nuclear plant are giving JMS free publicity discussing Babylon 5.
In 1998, Tom DeFalco penned "There Once Was a Spider..!" (Amazing Spider-Man #439), wherein a pair of archaeologists of a Future Imperfect find a webshooter and spend much of the issue explaining how their futuristic society thinks Spider-Man's life was like. Some of the many inaccuracies they believe in are that Spidey had a high-tech hideout with numerous trophies and spider-themed vehicles. Nearly 9 years later, a story of similar premise was used in Season 4, Episode 7 of The Batman called "Artifacts".
Mighty Thor #9 has a scene where the Silver Samurai sarcastically calls the title heroine "Sailor Moon."
The conclusion to the Secret Warps event had the Warped universe folding in on itself, several more times. During the first, where all characters were composites of four Marvel characters, we saw a fusion of all members of the Fantastic Four at once. But he was not called the 'Fantastic One', as you would expect - instead, he was The Wonderful One.
Squadron Supreme is a pastiche of the Justice League, and Marvel absolutely loves rubbing it in DC's lawyers' faces, ranging from Zarda calling Hyperion a "super-man" while explaining his origins to him, to Skymax telling the Exiles that "our league exists to serve justice" (emphasis theirs). When a version of the team becomes the US Government superheroes, not only do they add "of America" to their name, but because they're based in the capitol, they're called "D.C.'s greatest heroes".
Chris Claremont was a big fan of this. One of the alternate Earths the heroes visited during the "Cross-Time Caper" arc of Excalibur featured Lawyer Friendly Cameos from anime characters like the Dirty Pair (referred to as "A Lovely Pair"), while the M-Squad were very blatantly modeled after the Ghostbusters.
Destiny's real name is Irene Adler, a nod to the female thief of the same name from the Sherlock Holmes stories.
The Hellfire Club segment of The Dark Phoenix Saga is a Whole-Plot Reference to The Avengers (1960s) episode "A Touch of Brimstone". Because of this Jason Wyndgarde's name is a Shout-Out to Peter Wyndgarde (who played both the equivalent character in the original and Jason King) and Emma Frost's is a Shout-Out to Emma Peel. Later comics established the Black Queen of the London club as Emma Steed (a reference to Mrs Peel again and her partner John Steed) and a 17th century Black Queen was Diana Knight (Mrs Peel's maiden name was Knight and her actress was Diana Rigg) and her consort is Patrick Clemens (Patrick McNee played Steed and Brian Clemens wrote "A Touch of Brimstone".) The Steed and Mrs Peel comic returned the homage by having two variant covers which showed Mrs Peel, in her Queen of Sin outfit, in the place of Frost from the cover of an issue of New Mutants and Jean Grey from the cover of one of the Dark Phoenix issues of X-Men.
An issue of the second volume of New X-Men has Surge listening to "Sing for the Moment" by Eminem.
Polaris' civilian name, Lorna Dane, was taken from the novel Lorna Doone by R. D. Blackmore.
Sauron is named after J. R. R. Tolkien's Lord of the Rings villain of the same name. Sauron's origin flashback in X-Men #60 even has him explicitly mention the Tolkien connection while coming up with his villainous moniker.
The bridge of the Shi'ar ship that chases Lilandra to Earth looks... familiar. They even have similar uniforms, and a Prime Directive. A few pages later, Lilandra teleports to Earth, and Misty Knight comments that it even looks like the transporter effects.
The members of the Shi'ar Imperial Guard were famously modeled after various members of DC's Legion of Super-Heroes: Gladiator for Superboy, Mentor for Brainiac 5, Oracle for Saturn Girl, Fang for Timber Wolf, Smasher for Ultra Boy, Titan for Colossal Boy, ect.
Uncanny X-Men #153 has two shout-outs to ElfQuest: Kitty Pryde wears an ElfQuest teeshirt, and in the made-up story she tells there's a sprite named Pini who calls humans "bigthings", like Preservers in ElfQuest.
Spanning rather more than one issue is the first name of Rahne Sinclair, who can shapechange into a wolf, apparently a shout out to Rahnee the She-Wolf, the second chief of the Wolfriders. (Rahnee was first mentioned in ElfQuest #4, published in 1979, Rahne's first published appearance was in 1982.)
A novel and live-action movie (early 1980's), Wolfen, has perhaps influenced Wolfsbane of the New Mutants. The emphasis on both the sensory details of her wolf-form, and the link with Native Americans.
In the X-23 series Target X, Laura begins attending high school with her cousin Megan. Due to her, shall we say, abnormal upbringing, Laura thinks nothing of demonstrating her language skills to her French teacher by reciting a litany of ways to bribe and torture government officials, and later lists the exact amount of blood in the average human body and ways to kill someone in another class. The shout out comes from the depictions of the teachers: Jamie and Adam from MythBusters.
What If? #36 shows what would have happened had the Fantastic Four not gained their powers: Reed and Ben complete their space flight, and the foursome become well-known celebrities and do-gooders who are then tasked by the government to help solve a crisis caused by the Mole Man. As they enter an underground transport to the Mole Man's lair, Johnny asks Reed what he thinks they'll find on the other side.
Reed: The unknown, Johnny. But whatever it may be... We'll meet its Challenge.
Writer Fred Van Lente likes to do this in his comics, having characters quote or paraphrase classic movies or books. Few examples:
Abnett and Lanning again; once they ended up basically in charge of Marvel's cosmic characters, they seemed to love playing with the Alternate Company Equivalents they acquired, whether it was teasing the idea of Ego the Living Planet joining the Nova Corps (in reference to Mogo, the living Green Lantern planet), or Rocket Raccoon using "Brainiac" as a sarcastic term of abuse (like "Einstein" or "Sherlock") to Mentor, the Imperial Guard's Brainiac 5 Expy.
And while the Imperial Guard's influence is obvious, there's also smaller references in them. The symbiotic duo Warstar, the Guard's Triplicate Girl/Duo Damsel counterpart, are named B'nee and C'cil after Cecil the Sea Serpent and Benny.
◊ in issue #10 of The Avengers (Jason Aaron) is a direct homage to the cover of the first Marvel vs. Capcom game.
