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.)
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.
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.