In the Jackie Chan Adventures fic Queen of All Oni, after Jade becomes evil once more, we see that her parents neglected her almost to the point of abuse, painting her being sent to live with Jackie in a new light. In fact, she herself says that before her Start of Darkness, she would have thought being sent to Jackie's as the best thing that ever happened to her.
There is an entire genre of fanfic called angstfic, which makes the characters wallow in angst — especially if the original fic that the fanfic is based on is a wacky comedy or lighthearted. The usual victims are Pokémon and any comedy by Rumiko Takahashi. It helps that several characters have canonical tragic pasts, dysfunctional lives and relationships in the present, and bleak futures. If the canon series plays these for laughs, the viewers and fanfic writers may see them in a rather different light.
In one Magical Girl Lyrical Nanoha fanfic titled Behind the Smile, it is suggested that Hayate suffered sexual abuse in the foster care system before living alone, and her Skinship Grope tendencies were a way of warding off unwanted male attention.
In Crumbling Masks, a The Familiar of Zero fanfiction, Saito and Louise relationship of Double Standard: Abuse, Female on Male is taken seriously; but instead of the usual angst one might expect from this type of stories, it ends with both of them realizing they actually enjoy being in a S&M relationship and accepting themselves as the kind of persons who would enjoy that kind of thing.
Many, many Naruto fanfics turn Naruto's status as village black sheep into outright hatred and open, often homicidal abuse. So, that scene in the beginning where he's getting chased for vandalism by the equivalent of the Keystone Kops? People are actually trying to kill him over it. The small apartment he lives in by himself? A slum with no hot water that people frequently vandalize. His birthday? A festival in memory of the survivors of the Fox's attack on the day he was born, where he must fear for his life. The Hokage's advisors? Part of a village council made up of clan leaders (a.k.a. the parents of all his friends) who want nothing more than to exile him or publicly execute him. His favorite ramen stand? The only place in the village willing to sell him food. The reason Naruto's so dense? No teacher at the academy was willing to teach him anything. The reason a ninja wears a bright orange jumpsuit? The villagers wanted Naruto to completely fail at stealth and die on his first major mission. Yeesh.
In Horseshoes and Hand Grenades, we have Misa Torizaki whose most defining trait in Kamen Rider Fourze was her forcing Norio Eguchi to become Cygnus Zodiarts. She got away with it too. What happens here? Word spread about her actions and she's called "Swan Bitch" by people under their breath. Her backstory is her part of a rental company who ran away from home to escape her abusive and alcoholic step-father and the day she met Cygnus, she was going to be raped. Cygnus inspired her to make the Ugly Ducklings be a club that does good deeds and she severed her ties with the rental company...until they found out and put her through some degrading jobs. That, and probably holding onto the Zodiarts Switch, eroded her sanity that ultimately made her activate Norio's switch to become Cygnus.
Game Theory uses this both with elements from canon and the story itself. As an example of the former, Yuuno forgetting to tell Nanoha that he was human leads to a serious case of Poor Communication Kills instead of being played for laughs. As for the latter, the Running Gag of Hayate being obsessed with zombies turns out to be Foreshadowing the early involvement of the Mariage.
Death Note Equestria: L's personality and her relationship with Bon Bon becomes this when it's revealed that Bon Bon is actually a changeling. As Twilight explains, this means that Bon Bon was feeding off of L's emotions for years, essentially hollowing her out into a meat puppet.
The Facing the Future Series does this with the jokes about Danny wanting to be normal and him manifesting new ghost powers when it's revealed that his ghost half has sentience in his subconscious.
No Chance For Fate is this for two series at the same time. While in canon Sailor Moon at least tried to play its story serious despite comedy, Ranma ½ was simple sociopathic comedy. Taking away this coat of comedy (without actually removing humor) reveals how truly fear-inspiring parts of both canons are. On the Sailor Moon side, what was only implied in canon is now shown in its horrific glory. On the Ranma side, absurd canon plots are taken to their logical - and thus horrifying - conclusion. Shown dramatically with Happosai and Konatsu's backstory.
Quite a lot of Dark Fics in general run on revealing a work's lighthearted and whimsical elements to actually be fabrications hiding a dark and disturbing truth. One of the most well-known examples is The Rugrats Theory, which established that the babies and toddlers from Rugrats (with the exception of Dil and occasionally Kimi) were never alive (e.g. Tommy was stillborn, Chuckie died with his mother, and the DeVilles had an abortion) and that Angelica simply imagined them to be, which was a rather grim justification for how the babies managed to survive their parents constantly and obliviously neglecting them. Some versions of the theory went further and established the events of All Grown Up! as being drug-induced hallucinations Angelica experienced to try and bring her imaginary friends back and that Dil's bizarre behavior was a result of Angelica conking him on the head and giving him severe brain damage when he was an infant.
At least one Code Lyoko fic takes the Ripple-Proof Memory possessed by the heroes and delves into certain more realistic consequences, including having characters react badly to nearly being Forced to Watch bystanders die while being powerless to stop it and having a severe assault that was Retgoned by the Return to the Past still be traumatizing to the victim, with the added wrinkle that now the assault in question never happened in the first place.
Pacifica: And my parents drag me to these big publicity things where all I'm supposed to do is wave and watch everyone else have fun... Dad wants me to take over the family's business someday, but I'm not sure if I want to do that, you know?
In the third edition of the anthology series Halloween Unspectacular, Jazz is taken in as an apprentice by the magician Madame Athena, to learn magic. This continues all the way through to the fifth edition, where it's revealed that Athena foresaw a coming disaster that could only be averted by sacrificing a person of the Fenton bloodline (due to them being descended from King Arthur), and Jazz is the only candidate due to Danny's blood being tainted by his ghost powers.
A number of Marvel Cinematic Universe stories such as To Intervene reimagine the post credits scene in Iron Man 3 where Tony tells the entire story to Bruce as the moment Tony decides none of the Avengers are actually his friends and another nail in his growing depression.