The episode "Hurricane Fluttershy" had a flashback to Flight Camp when Fluttershy failed a flying test and crashed, after which she was surrounded by her class mates and subjected to a Circle of Shame. This makes a simular flashback scene in Getting Back on Your Hooves were a near identical incident happened to Rainbow Dash not only plausable, but even more disturbing. Even the author was a bit freaked out by this.
At one point in "The Crystal Empire Part 2", Twilight uses dark magic, which causes her magic to go from magenta to black, to find a secret underground staircase made by King Sombra. In the fanfic Pages Of Harmony, written several months before The Crystal Empire aired, Twilight's Mad Scientist Laboratory is reached through a staircase very much like Sombra's, and her magic's color changes from magenta to black.
The Fanfic Trixcord involved Trixie, after being terrorized by Discord, run into an open street where she gets her neck snapped being run over by a carriage (she gets better). The episode Magic Duel had an insane Trixie with semi-fourth wall breaking powers declare she did not trust wheels.
While not noticeable to the reader at first, in 'Nexus' the scene where Dante hugs his nephew could count, especially if you read the pre-cursor’s bittersweet ending. It was Heartwarming Moments, since the character showing the emotion was Dante, until Jack ruined the moment by (unknowingly) reminding Dante that he didn’t remember him at all. Then Dante just looked depressed.
The Katawa Shoujo fanfic From Shizunes Perspective was written before the release of the full game. Several of the twists come off in a new light when you consider what happens in Shizune's route.
Early on, it's revealed that Shizune is bisexual and Misha is heterosexual; Shizune mentions that she once confessed to Misha, but takes her rejection due to Incompatible Orientation in stride. In the full game, the situation is reversed; the lesbian Misha confesses to the heterosexual Shizune, and is rejected, but Shizune wants her around as a friend, leading to tension as Hisao gets closer to Shizune.
Midway through the fic, Shizune finds out that Misha and Hisao are in a relationship when she finds them having sex, and is upset because they never told her. In the game, choosing to give Misha Sex for Solace gets you Shizune's bad ending, and Shizune never even finds out.
Later in the fic, Shizune vents to Emi about how her deafness prevents her from getting school gossip, which, in serving as Student Council President, earns her a reputation as bossy. In the full game, Shizune's well-intentioned efforts to inspire the student body to act, hampered by her communication problems, drove the rest of the council besides Misha away, and resulted in her being quite lonely.
In DC Nation, issues #20-#21 of the New Teen Titans comic (May-June 1986) are affectionately known as "The Mission from Hell." The Titans were (temporarily) mostly broken up after incidents involving or happening roughly around the time of Crisis on Infinite Earths. Wonder Girl, who is left in charge with an empty nest, calls in Aqualad, a newly-minted Flash, a Hawk without Dove, Jason-Robin and her ex-boyfriend Speedy. At the request of King Faraday, they help to protect a peace conference which is being threatened by Cheshire. Yes, the Cheshire Speedy had a relationship with. This was where it was discovered they had a child together. Issue #21 closes on some supposed to be heart-warming reconciliations between Terry Long and Wonder Girl and also Speedy and Cheshire, including him getting to hold his daughter for the first time. Also, Wally getting to explain his new role as The Flash to his hero-avoidant then-girlfriend Francis Kane. Now, look at these events through the lens of:
Wonder Girl and Speedy still being in love, but not pursuing those feelings due to the machinations of Dark Angel.
Aqualad being suicidal after the loss of Tula.
King Faraday being mind-controlled by Diablo to be Gamemaster.
Wally-Flash not knowing what he's doing and trying to imitate Barry Allen. His behavior around this time is often-cited by his peers in-game as to why "growing up and becoming JLA members" is no longer concidered an option if the Titan in question wants to keep their sense of self.
Wonder Girl having a miscarriage after a fight with Cheshire when she hadn't known she was pregnant which actually stopped Aqualad from killing himself. After getting treatment, which she swore him to secrecy about, the next day she finds out about Lian's birth.
Jason being the voice of reason among his older, more experienced peers. In Nation-canon he received a statue in the memorial hall upon his death for this and the work to free Raven, which is different from in pre-reboot DC-canon.
Having Speedy, Wonder Girl and Flash return to Cheshire, Terry Long and Francis Kane with the idea that this is a relief to them. In Nation, all three couplings have been potrayed as abusive and/or unhealthy relationships.
Realizing that Lian would have been concieved just about the time of Wonder Girl's wedding to Terry Long with the compressed timeline. Can you say rebound?
In The Prayer Warriors, during the attack on the temple of Zeus in "The Evil Gods Part 1", Percy Jackson encounters a woman being raped, killing her rapist but sparing her because she cried out loudly enough and indicated that she was not enjoying it. In "Threat of Satanic Commonism," when Ebony gets raped, he not only kills the rapist, but also kills her, showing that he meant what he said.
In How I Became Yours, Toph, after hearing that Sokka revealed Zuko and Katara's love child Kuzon's existence by sending a letter to Zuko, says "Katara is going to kill you... I can only imagine what Mai will do to Zuko...". A demonized, Out of Character, Yandere Mai poisons Katara, causing her to miscarrynote it had happened at the time, but Katara was unaware of Mai's involvement at this point in the story, and later tries to kill her herself.
In the sequel comic Rise Of The Agni Army, it's pretty much a given that Zuko's murderer was indeed Mai, who somehow survived being bloodbent to death. Brr...
It's astonishing how similar Zuko confronting Mai about hiding the existence of his love child with Katara by hiding her letters until a servant showed them to him is to Ozai confronting Ursa in a flashback in The Search over Zuko being Ikem's son rather than Ozai's, something he learned by the servant Ursa entrusted to deliver her letters betraying her and giving them to Ozai. Zuko may be turning out more like Ozai than he thought here even if Ozai isn't his biological father.
There's bucket loads of Foreshadowing for the season 1 finale of Children of Time, and plenty of moments within the three-part finale itself that get worse later on.
“Not if you do not wish to truly experience your role and sleep on the street...” Which Beth Lestrade actually ends up doing in the next episode while on the run with the Irregulars.
“I should have cuffed you to the railing back at Baker Street.” Sherlock Holmes cuffs Beth to the cab door just half an hour later, which starts the ball rolling on a world of trouble between the two.
Not to mention the use of Vincent Starrett's famous Sherlockian poem as a Motif for the finale. Sherlockian readers will never think of the words "always 1895" the same way again.
In The Spoils of War Bellatrix declared when she was six that one day she'd live in the biggest castle in the world. When Harry and a sane Bellatrix review her memories, she notes she was right. The biggest castle in the world is Azkaban.
In an author's note for the fanfic New Lifenote Which, just as a warning, has a pairing that many people would consider Squick the author mentions that he is serving in the U.S. military, so updates will be sporadic because he doesn't have access to a computer. The update after that wasn't a true chapter, instead, it was a note from the author's cousin that he had been killed while serving in Afghanistan.
Note that as of 2014, the author's cousin has deleted all of the chapters to the story except for the first one, but the reviews still provide evidence for this.
In Thrones Of The Four Pillars, the Ghibli Hills is a Miyazaki-themed world that is destroyed by the Big Bad. This gets harsher when it was noticed that Studio Ghibli closed its doors (it went under reestructuring process though but it doesn't make it less harsher).