Black Hole has a mysterious disease that causes bizarre mutations. Even though it takes place in the seventies, the fear, paranoia and prejudice portrayed make it clear that it's a metaphor for AIDS.
Buffy the Vampire Slayer: One comic has Faith first hiding in a Berlin bunker, then escaping by train. However Book Dumb she appears, she recognizes the similarity to the Holocaust enough to be disturbed by it.
Batman: Black and White: "Perpetual Mourning" depicts Batman performing a post mortem examination of an unidentified female murder victim. When he begins the examination by picking up her hand to examine her injuries, it's framed like a swain bowing over a lady's hand to ask her for a dance.
Superman: After Superman gets temporarily de-powered in the events of Infinite Crisis, Lois' assurances that she loves him, that it's perfectly understandable, that she's sure he'll be back to normal in no time, and even that she loves him for who he is and not how well he can perform, sound rather like Superman is having a different kind of performance issue.
Disney Ducks Comic Universe: "That Ol' Soft Soap" has Donald aggressively expanding a soap business by ever more elaborate marketing and packaging schemes while diminishing the actual content. The packaging is aimed at soap collectors, two of which are shown fighting over whose limited-edition bar is the rarest. This inevitably ends in a crash.
Forever Evil (2013): In Issue 1, to enhance his powers with kryptonite, Ultraman crushes, burns, and inhales the kryptonite vapors. He then boasts about how he's the strongest before flying off to find some more.
The House of Mystery story "The Demon Within" tells the tale of a young boy who discovers he can transform into a monster. His family is embarrassed and ashamed by his ability, largely due to concern over how it will affect their social standing, to the point that they forbid him from using it and take drastic measures when he continues to do so, ending with the boy undergoing electroshock therapy and then a lobotomy so they can continue to appear normal to their community. It serves as a metaphor for pretty much any family that tries to hide or suppress their "unusual" children (e.g. neurodivergent children) to make themselves appear "normal".
In "Judgment Day (EC Comics)", an examiner comes from Earth to see if a planet inhabited by sapient robots is ready to join The Federation. It's revealed that the robots are split into two groups identical except for the color of their outside casing, and the educational programming given to each color. One group of robots is given less useful programming, forced to live in inferior housing in a segregated part of the cities, relegated to less desirable jobs, etc., all based on the casing color. The examiner is forced to flunk the civilization, and the guide complains that he is "only one robot" who can't change the system. The examiner consoles the guide by mentioning that Earth used to be like this too until its people got their act together. Then the examiner gets into his spaceship, takes off his helmet, and is revealed to be black.
Black Panther's debut issue in The Avengers involved the character being falsely accused of murdering his teammates, and subsequently going on the run. While the hero's race is never brought up, it's hard not to read the story as a metaphor for racial profiling.
Civil War (2006): The Aesop can best be summed up as "if you aren't doing anything wrong, you have nothing to hide". Any American who hasn't been living under a rock knows why that sounds familiar (and why it is better phrased as "If you aren't doing anything the government/media think is wrong, you have nothing to hide", a quite different concept).
Iron Man: In one arc, the armor is struck by lightning; this, in combination with Y2K, made it sentient. Tony wants to transfer its mind to something less dangerous, or kill it, but then the armor tells him that it loves him. "How would you define the feelings I have for you? Because, if what I learned from your mind is true — it feels exactly the same as what you feel — for Ms. Fujikawa." Tony then decides to see if he can be a better Iron Man while in the sentient armor, but can't control it... The armor claims to be protecting Tony, and then it stops letting his friends over. He puts on an older Iron Man suit to try and escape, whichenrages the armor, and it takes him to an island and tortures him, then apologizes... Evidently, Steve Rogers taught Tony how to escape from being tied to a tree, and the thought of him gives Tony strength. Still, Tony has a heart attack during the fight, and the armor, horrified, does a Heroic Sacrifice/Redemption Equals Death. Among many comic!Iron Man fans, the sentient armor is generally called "Tony's abusive boyfriend".
Ms. Marvel (2014): Kamala normally tries to resort to minimal force even against animals... but she doesn't take kindly to one of her first powered villains turning out to be an Inhuman supremacist. Her rant against her, focusing on how she refuses to let one person's evil turn the world against everyone like her, is given a particular degree of weight by her being a Muslim Pakistani-American.
Kamala: It's always the same. There's always one group of people who think they have special permission to terrorize anybody who disagrees with them. And then everybody else who looks like them suffers. Not again. NEVER AGAIN.
In issue fifteen, after Kamala is kidnapped by Kamran, he explains that everything that made her vulnerable was something she did of her own free will, despite the fact that when Kamala realized something was up she repeatedly insisted that he stop. She even wonders if what happened really was her own fault. It sounds a lot like a sexual assault victim being told that she should have been more careful when confronting the person who assaulted her. G. Willow Wilson tweeted that "I wanted to talk about consent in a fun, accessible way, without making the world into a terrifying place."
New Avengers: The Hood's ambush and No-Holds-Barred Beatdown of Tigra while she's alone in her bedroom has some pretty blatant parallels to a rape, complete with a battered Tigra lying sobbing on the floor after it's over. When he sneaks up in her bedroom in the second annual, the scene also has rape parallels, especially since she Sleeps in the Nude and has only a Modesty Bedsheet on while most of his gang is clearly leering at her. A later arc in Avengers Academy drives it home even further when Tigra discusses her assault on live television and states that it's not her shame to bear, but her attacker's.
The titular bird-being is weakened and needs energy to restore itself. So, it crawls onto Scott's sleeping body, narrating how it "need[s] so much". This led to fans nicknaming it a "cosmic stalker." Other scenes are even better.
Phoenix Force:[to Jean] He always wanted you. Maybe that's why I like being you so much.
In the finale, Cyclops shoots his Eye Beams directly at the Phoenix, who's flinging her limbs outward and screaming ecstatically; "Yes! More!" The stream of Cyclops's power, incidentally, lands right on the Phoenix's cleavage.
She-Hulk: Apparently, transforming from her puny human state into the green goddess is the equivalent of sexual orgasm to her, as was showcased in not only the Ultimate incarnation, but on the classic 1990s cartoon as well, which was supposedly for the "younger" crowd.
In their first appearance, three skrulls were hypnotized to shapeshift into cows. Skrull Kill Krew features a group of humans who developed shapeshifting abilities (but also became mentally unstable) after eating burgers made with those cows' meat, jokingly called "skrullburgers". The fear of tainted meat entering the food chain was clearly a reference to the mad cow disease scare during the mid-nineties.
In the past, the situation of mutants was compared to ethnic minorities, and was originally meant as a metaphor of the Civil Rights movement of the 1960s. Since the '70s, however, they've shown a tendency to make discussions of being a mutant sound like they're about LGBT rights, particularly after racial minority groups complained of the co-option of their struggle for characters who, as a whole, are mainly white. In any case, LGBT is a better fit — mutation, after all, develops at puberty, with parents varying from supportive to... really not, and a lot of the anti-mutant groups are religiously based, calling mutants abominations before God. X2: X-Men United hammered this home with the famous line, "Have you ever tried not being a mutant?"
Some stories have taken things even further. The systematic incarceration and extermination of mutants in "Days of Future Past" draws strong comparisons to The Holocaust, while Magneto often cites the persecution of the Jews by the Nazis as part of his motivation. The first X-Men film makes this connection even more explicit by opening with a scene of young Erik arriving at Auschwitz, where his powers first awaken.
Uncanny X-Men (Chuck Austen) ends with a story in which Magneto's body is returned to Genosha. This was published in 2004, just after the finale of New X-Men, in which he devastated parts of New York and hundreds of civilians died. The story shows a wrecked Statue of Liberty and superheroes searching rubble for trapped survivors. Nick Fury and Wolverine both get angry rants about Magneto getting any sort of burial, and are furious with Xavier for arranging it, with Fury suggesting Magneto should be chopped up and fed to dogs. In context, it's very easy to read as an analogy to The War on Terror and 9/11.
In Jonathan Hickman's run, when both Storm and X are showing the resurrected X-Men and loudly declaring they've conquered death (with Storm even calling them brothers and sisters), as well as the cheering crowd, the Mutant race starts to look like a cult.
My Little Pony: Friendship Is Magic (IDW): "All in Moderation" focuses on a controversy over sugar that's very closely patterned after Prohibition, with sugar replacing alcohol and worries over health issues replacing concerns over drunkenness. The visuals are otherwise identical, including a pseudo-Puritan firespitter heading the Anti-Sugar League and an underground speakeasy where ponies gather to enjoy sweets (complete with Spike in a fake mustache playing the pianoforte, Fluttershy Sitting Sexy on a Piano while singing in an opera gown and Rainbow Dash somehow managing to convincingly replicate the effects of drunkenness after going nuts on milkshakes).
Rorschach (2020) takes place in the year 2020 of an Alternate History established by Watchmen, and while much had diverged since then, there's an uncomfortable series of constants through the main instigators of the plot: a small group of domestic terrorists from rural America who — shattered by their trust in the government and believing an extensive conspiracy theory that they were being run by a secret supernatural cabal — took it upon themselves to attempt murdering an important politician to "free" America and restore it to greatness. Their ethos is ultimately the same as far-right extremist movements of real life, only instead of lizard people, they believe the government is run by psychic squids.
In Paperinik New Adventures #35 we see how the Evronians consume the emotions they absorb: it really looks like a drug addict getting his fix.
X-Wing Rogue Squadron: The Anti-Endor Association, a pro-Imperial student group at the Mrlsst Trade and Science Academy, say the Battle of Endor never took place, with the Death Star still around and the Emperor's alive. They also say the Rebels destroyed Alderaan and no Jedi exist. All of the (true) reports about it they ascribe to Rebel propaganda. Given the Empire's Fantastic Racism and Putting on the Reich they bear a resemblance to Neo-Nazi Holocaust deniers. Additionally, several of the Rogues protesting that they shouldn't be able to spread nonsense echoes real reactions to this, along with the Academy's policy of permitting this on freedom of speech grounds.
Zatanna: Everyday Magic: Constantine's "curse" that he got from sleeping with the villainous and promiscuous Nimue is treated as an allegory for getting an STD from an ill-advised one night stand.
Comic Strips
One Calvin and Hobbes strip is an illustrated poem about aliens who arrive in a spaceship and steal the ocean and the atmosphere, responding to the "Earthling despair" this causes with "We prefer your extinction / To the loss of our job."
Calvin: That's my science fiction story. Think it's too far-fetched?
Dilbert: In one comic, Tina gets in trouble for sending a dirty e-mail and Catbert decides to look the other way if she rubs his belly. It has a hell of a subtext:
Tina: This seems so wrong. Catbert: Try using both hands.
The Far Side: One strip has the Big Bad Wolf on a psychiatrist's couch, confessing that "on and off I've been dressing as a grandma ever since".
Liberty Meadows combines this with Heh Heh, You Said "X"here, where Ralph brags about his new invention — a fossil-finding apparatus that can find bones in a hundred-meter radius, which he calls the Boner 3000 — while holding it... rather suggestively.
tells the tale of a young boy who discovers he can transform into a monster. His family is embarrassed and ashamed by his ability, largely due to concern over how it will affect their social standing, to the point that they forbid him from using it and take drastic measures when he continues to do so, ending with the boy undergoing electroshock therapy and then a lobotomy so they can continue to appear normal to their community. It serves as a metaphor for pretty much any family that tries to hide or suppress their "unusual" children (e.g. neurodivergent children) to make themselves appear "normal".
