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 metaphore 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.
EC Comics: In "Judgment Day", 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.
Forever Evil: 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.
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.
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 him, focusing on how she refuses to let one person's evil turn the world against everyone like him, is given a particular degree of weight by her being a Muslim Pakistani-American. G. Willow Wilson specifically described the events of #15 as "I wanted to talk about consent in a fun, accessible way, without making the world into a terrifying place".
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.
New Avengers: The Hood's attack on Tigra has some pretty blatant parallels to a rape, complete with a battered Tigra lying sobbing on the floor after it's over. 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 bare, 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 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. The first film trilogy 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 sites 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.
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 goings nuts on milkshakes).
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.