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.)
Child Of The Storm has a fair degree of the usual MCU themes shown in the post Avengers films, 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?
It also touches on 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.
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.
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 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.
In Stargate Atlantis, the main villains the Wraith feed by sucking out people's life forces through an orifice in their hands. That this orifice resembles female genitalia has not gone unnoticed in the fandom.