The True Monster by lord of the land of fire includes a Whole Plot Reference to World War II. (Warning: some content is NSFW. Sex scenes are not essential to the plot, so it is possible to skip over them without missing anything.)
A fair degree of the usual Marvel Cinematic Universe themes shown in the post The Avengers (2012) films feature, but Operation Overlord is very familiar. MI6 is destroyed, with thousands killed. The response is a stripping away of usual protocol to allow SHIELD and its allies to enact a No-Holds-Barred Beatdown of HYDRA, with every base but one being destroyed, but not quite getting to the leaders, who hole up in secret, right under the noses of the British government, and respond with an attack designed to devastate London. Stripped of its fantasy/superhero trappings, does this or does this not sound like 9/11, the invasion of Afghanistan and declaration of an international 'War On Terror', arguably doing more harm than good, partly leading to the London Bombings?
What Harry Dresden suffered at the hands of the Red Court, with him saying flatly, "They did things to me," which draws a horrified silence and a supportive squeezed hand from his companions, emphasising the gang rape connotations of what happened to him.
Chapter 66 has Sean Cassidy bluntly compare what Riddle's diary did to Ginny to grooming by a pedophile over the internet, right down to the rape and murder (in terms of the draining of her lifeforce) afterwards.
In After School Activities "Ryuuga" has been missing classes so Light has to bring him up to speed on their latest Psych lessons. The topic of the lesson is cult leaders. The Irony of the situation is not lost on L.
Gevanni: No you don't understand, this other guy was watching him too and he then suddenly whipped it out right there! Near: Ugh! You called me for this? Gevanni: This is important! He reached into his pocket and whipped out aŚ Near: NO! Gevanni: Death Note!
Aftershock describes Tidus hugging Yuna just before he fades away:
As his lips pressed against her hair, she closed her eyes, savoring the warmth of his body against her back; and then, it was almost as if he melted into her. A heat unlike anything she had ever known, save perhaps for that night at the spring, enveloped her as he filled every corner of her being for a single moment in time. It was all she could do not to cry out when he pulled away...
In Son of the Desert Trisha has to hide in a small crawl space whenever the military visits Reseembool to avoid being rounded and killed with other Ishvalans, and later a law was signed deeming that anyone with Ishvalan heritage or ancestry was to be killed. I'm sure this has nothing to do with the Holocaust.
The Meaning of One series by Sovran features a soul bond between Harry and Ginny. Let's see, they are different from either of their parents, they didn't choose their circumstances but are happy with them, they face initial hostility from some of Ginny's family, especially Molly, who (unjustly) suspects them of engaging in various perverted acts, and they have to keep their relationship a secret from all but their family, closest friends, McGonagall, and Dumbledore. Could this, perhaps, be an allusion to the experience of gays and lesbians?
In Before I Sleep, the scene where Silas is beaten to within an inch of his life, and eventually fatally shot, while out on a date with Dessie is disturbingly reminiscent of a young black man being attacked for going out with a white woman, especially due to the setting and time period the story takes place in. The parallel is made even stronger when his attackers try to rationalize it by deluding themselves into believing they were 'protecting' her.
In The Assassination Of Twilight Sparkle, Twilight's coronation apparently sparked a backlash among the people who were afraid of the change and what it would bring to their lives while the few people who tolerated it kept quiet. More than a little like how the fandom reacted when it happened in canon, eh?
Magnetism has a ball with this in its fourth chapter. We keep seeing Angel's imaginings, which sound very sexual but end up being decidedly not, never mind the dream at the beginning, which ends when Fluttershy served breakfast in bed instead.
My Little Unicorn: The Unicornicopians settle in and remake Equestria, treat its original citizens as inferior and suppress their culture and language, particularly making them use "everybody" instead of "everypony". All that's missing is a residential school!
Little Sun has a rather dark scene where Princess Celestia tortures, and then launches a full-scale slaughter on, members of Nightmare Cult, a murderous group of ponies who pledge allegiance to Nightmare Moon, following an assassination attempt on her and her daughter Sunset Shimmer at the latter's birthday party. The cult is clearly a stand-in for terrorist groups like Al-Quaeda and ISIS, and Celestia's moral crisis in dealing with them is not unlike the U.S. government's controversial decisions regarding terrorism.
Beyond The Winding Road has a moment early on where Lewis has to tell his family he's the reincarnation of a famous martyr, and he's afraid they won't believe him or treat who he is as real because his past identity and memory issues were diagnosed as Dissociative Identity Disorder (AKA Multiple Personality Disorder). But before we know much about this, Lewis explaining who he is to his parents can easily be read as him coming out. In fact, that's exactly what his mother thought it was.
Despite essentially being an extended epilogue focused on the aftereffects of the manga, Beyond the Winding Road can also be read as an exploration into how people with disorders affect those around them and how different approaches to dealing with disorders can affect the people who have them.
In Persephone's Waltz, the audience knows full well that Homura has no intention of harming Madoka and just wants to keep her safe. But that doesn't stop it looking like she wants Madoka as a Sex Slave when she kidnaps her and imprisons her in an underground room with Homura as her only human contact. This is exactly what Sayaka fears, and is why she's so desperate to find her.
A superpower gets involved in a foreign civil war that it partially started in the first place and invades the galaxy, prompting another major superpower to invade in response, and the conflict quickly bogs down into bloody stalemate. Korea? Nope, definitely not.
According to Word of God, the Jewish Republic is a far right wing society obsessed with Jewish racial purity and often exterminates worlds with toxic gas. Gee, I wonder what major world event that is an ironicreferenceto.
At Chirei plays out the drama of Koishi leaving to explore the surface as almost exactly like a divorce, with Okuu and Orin caught between their two Parental Substitutes, desperate to make one of them happy again and to get the other one to return. At the same time, Koishi sealing her Psychic Powers is very reminiscent of dementia.
"The inside of my head is light... like it's gone somewhere. The old me is gone. She's gone somewhere else, far away."