"I've seen a lot of backstories written about how Equestria is simply a post-apocalyptic Earth set in the distant future. I decided to expand on it in a much less... grimdark fashion."
These quotes from Twilight Sparkle in the original story were meant to be joking, but became way less funny with the numerous stories that have the barrier being intentionally expanded as a means to force ponification, and any stories that have the PER in them.
"Now, I'm almost positive all of you are here because you want to become a pony. This is a fact. You don't come here because you don't want to be a pony, unless someone forced you at gunpoint, but that's a different story."
"Our plan is to ponify you, the sooner the better. Expect this to happen when you least expect it."
On May 30, 2010, a reviewer by the name of Robert Donahue left a comedic review on ''New Life. The author later died in Afghanistan serving in the military. The review in question?
"hey man its cool i understand with war and stuff. just dont die and write more for us ok lol"
The Arrow story Red featured a romance between Sara Lance and Thea Queen, but since it was revealed on the show that Thea killed Sara while under the effects of a mind control drug, it became highly inappropriate, leading to the story's deletion.
In Kyon: Big Damn Hero's prologue Kyon tells Ryoko that she is the most reasonable person to ever try to kill him but that he remembers that time she stabbed him all too well. This becomes hilarious later on when we learn another two of his classmates tried to kill him during separate occasions, and when he's fighting for his life against some Yakuza.
The fan-fiction writers for the site Ghostbusters West Coast have a particularly bad record for this. One story had Michael Jackson as a werewolf who got savagely beaten up by the main characters and then arrested for murder, and another had a character explaining that he almost ran over an old man because "I thought you were Ted Kennedy."
In From Shizune's PerspectiveShizune once tells Misha "Eat Me", prompting Misha to quip that she told Shizune that she didn't go that way, to which Shizune responds with a nonchalant "Your Loss". In the actual visual novel, the full version of which was released after the fic Misha is a lesbian who confessed to Shizune and got rejected, but Shizune continued to keep her around, counting on her for her friendship. Misha takes the rejection and Shizune's continued presence quite hard, and these issues come to a head at the end of Act 3, potentially ending their friendship and Hisao's relationship with Shizune if you make the wrong decision.
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 miscarry note 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, Mai apparently is the one who killed Zuko.
In a 2009 episode of Calvin and Hobbes: The Series, a panicking Calvin claims that "Japan is going to fall into the ocean!" in 2011, Japan and the ocean found themselves in a rather unpleasant relationship.
In the anniversary chapter of You Got HaruhiRolled! (written in July of 2010) one of the many ridiculously over-the-top things to happen in the SOS Brigade and Anti-SOS Brigade's fight is that Mikuru somehow gets into position to smother Fujiwara with her breasts, almost killing him before the others intervene. Of course it was only a gag then, but once the eleventh novel of the source material is released, it is revealed that Mikuru and Fujiwara are siblings. Now it becomes so much more disturbing.
Akane's Pervert Revenge Mode against the Hentai Horde in canon becomes a lot less funny and a lot more justified in Ranma Saotome, Chi Master where it's revealed one of her greatest fears is that she'll lose against them and be gang-raped.
This webcomic◊ essentially shows a playthrough of Persona 3 in which Minato goes through the game acting like a Jerk Ass to all his friends, and as a result, doesn't maximize any of his Social Linksnote Your Fool, Death and Judgment links automatically max out if you reach the good ending, something that is very much Played for Laughs. In particular, after Keisuke leaves the art club, Minato steals the credit for his painting by crossing out Keisuke and writing Minato instead. In Persona 5 you learn that Yusuke's guardian Madarame has been doing this to him for years, and even let Yusuke's mother die so that he could steal her painting and exploit Yusuke's talent.