The "Bright Lights" series of My Little Pony 'n Friends featured a pop star, modeled after Michael Jackson, whose manager stole fillies shadows as a form of Applied Phlebotinum. Years later, Michael Jackson began to face accusations of taking indecent liberties with children.
In Ed, Edd 'n' Eddy, after the Eds wrongfully accuse Jonny of being a "serial toucher" and sentence him to rolling down a hill in a giant tire. When Double D calls Ed out on this, Eddy calmly responds "You know what they say, a little childhood trauma builds character." Given that The Movie reveals the abuse at the hands of his brother, Eddy might honestly believe it to be true.
The SpongeBob SquarePants episode "The Smoking Peanut" is about a clam at a zoo going berserk after SpongeBob throws a peanut at it. Several years later, a tiger escaped from its habitat and attacked three teenage boys at the San Francisco Zoo. Some people believe the boys had taunted it. Also in that same episode, the clam throws one of the zookeepers while on a rampage. In 2010, an orca killed one of its trainers at Seaworld.
In the Family Guy episode "Dog Gone", Brian unties a large dog left outside, only for said dog to violently attack and kill a smaller dog (before being shot to death by cops), this scene became even more uncomfortable to watch after something similar happened in real life.
In the same episode, the ending where the family believes Brian died in a fire is this when you consider the events of "Life of Brian".
Peter's "Gary the No-Trash Cougar" character breaking into an elementary school cafeteria and threatening children with a gun in order to get them to throw out their garbage in the episode "Blind Ambition" definitely seems harsher as a result of the Sandy Hook Elementary School shootings in December 2012.
Three weeks after "Turban Cowboy" aired, the Boston Marathon Bombings happened. Suddenly, the main plot of Peter converting to Islam and being a pawn in a terrorist attack and the cutaway joke of Peter plowing through runners in his car aren't so funny (in a sick way) anymore. Even Seth MacFarlane called out having his episode being used in a video that "predicted" the bombings would happen. The episode was banned from airing on FOX and Hulu, but has come back on cable (TBS and Cartoon Network) and can be seen on Netflix's streaming program (of course, this was months after the Boston Marathon attack was news).
The infamous episode "Seahorse Seashell Party" angered many fans due to the Family-Unfriendly Aesop that "staying with your abusers is good for them", and the very next episode "Screams of Silence: The Story of Brenda Q" was a Very Special Episode that made it clear that staying with an abuser is bad. This led to many criticizing the show as being hypocritical or offering a hackneyed apology to those who were offended. It should be noted that "Seahorse Seashell Party" (along with the loosely related episodes "The Hurricane" from The Cleveland Show and "Hurricane!" from American Dad!) was to originally air 5 months earlier (and not followed by "Screams of Silence: The Story of Brenda Q") before being pulled due to a series of tornadoes in the southern US several days before the original airdate.
In Avatar: The Last Airbender, in "Tales of Ba Sing Se", a clip is shown where Iroh is crying over the loss of his son. Before the episode was aired (but after the rest of the voice-overs for that season were completed), the voice actor for Iroh, Mako, died.
The end of the episode "All Singing, All Dancing'' had Snake bothered by the family's constant singing and threatening them with a gun. To stop the end credits music he fires, just as Phil Hartman's name appears. Hartman would be shot to death by his wife months later.
Speaking of The Simpsons, it's a little unsettling watching the musical version of A Streetcar Named Desire where they call New Orleans "The Sodom and Gomorrah of the Mississipi" after Hurricane Katrina. Because of this, UK broadcaster Channel Four had to make a public apology for airing the episode around the time that news of Hurricane Katrina's destruction was still fresh in everyone's mind and it has become a Banned Episode.
Try watching "Bart of Darkness" where Bart thinks Flanders killed his wife now that Maude has been Killed Off for Real on the season 11 episode "Alone Again, Natura-Diddly". Or "Realty Bites" where Marge thinks the Flanders got killed in a house that was once the scene of a grisly murder involving a jockey and his wife. Or "The Springfield Connection," in which Homer tricks Flanders into thinking his wife and kids are dead by putting police tape outside his house.
Beyond Blunderdome had special guest star Mel Gibson turning to Homer of all people for advice on how to improve his remake of Mr. Smith Goes To Washington, simply because Gibson happened to read an angry letter that Homer wrote about it from a test screening and became convinced that Homer was the one person who was actually being honest with him, and despite everyone telling him otherwise Gibson ends up going along with Homer's rather childish and stupid suggestion of making the ending an ultra-violent action movie type climax, which turns the film into a critical and commercial disaster, seriously damaging Gibson's reputation and star power in the process (the episode ends with Gibson angrily kicking Homer out of his limo once he realizes that Homer really is just a stupid jerk and not a valid critic). A few years later Gibson's life and career fell apart when he couldn't cope with the negative critical response to his very bloody The Passion of the Christ. On the other hand, all of this is Hilarious in Hindsight because this episode depicts Mel Gibson as being beloved and everyone fawning over him.
Many Simpsons episodes featured bullying as a comedic plot device — Harsher in Hindsight due to today's public awareness about the emotional harms of bullying, and several tragic cases where kids felt driven to suicide or violence due to constant bullying. If you're concerned over how cruel kids are these days, or if you were a victim of bullying, the following episodes won't be considered funny to you:
"Bart the General" — though at the end Bart warns that violence is never the answer
"Eeny Teeny Maya Moe" (the subplot about Maggie being bullied by babies and maybe the main plot about Moe cracking jokes about his girlfriend who is a female dwarf, but Moe does learn his lesson on not to be so shallow after Homer tells him that, despite what happened, he found someone who actually loved him and Homer does save his daughter from being bullied).
In "$pringfield (Or, How I Learned to Stop Worrying and Love Legalized Gambling)," one of the many failures at Burns' casino is that Siegfried & Roy expies Gunther and Ernst are mauled by their own tiger while entertaining. Ten years later, it happened in real life to Roy Horn. The writers mentioned in the DVD commentary that the incident was bound to happen sooner or later and they were amazed when it did.
The beginning of the episode "Lisa vs. Malibu Stacy" note The episode where Lisa creates a doll that's actually a good role model for little girls while Grampa gets a job at Krusty Burger so he can be young and hip, only to learn that God wanted people to get old so they can criticize everything He's doing wrong where a bunch of elderly fans attack Matlock (Andy Griffith) and Grampa Simpson swipes his heart medication (and the subsequent shot of Andy Griffith getting rushed to the hospital) is now not so funny anymore thanks to Andy Griffith's real life death from a heart attack in July 2012.
During the cold open to the 2008 Halloween episode, Homer tries to vote for Obama, but the voting machine keeps repeatedly choosing Republican John McCain. Four years later many machines have been reported of doing the same supposedly in favor of both Obama and Mitt Romney (though this time because of poor calibration).
"A Totally Fun Thing That Bart Will Never Do Again" has Bart sabotaging a cruise ship so his dream vacation will never end, causing the ship's passengers to endure progressively worse conditions. In February 2013, the Carnival Triumph blew out its engines and was stranded for four days in the middle of the ocean before it was rescued.
"Sleeping with the Enemy" has Lisa being concerned about her weight and going to a store that sells ultra-thin clothing below size zero. This becomes even more painful after the CEO of Abercrombie & Fitch revealed that they don't make clothes higher than large because it discriminates against larger people.
In "Treehouse of Horror XII", at one point during the segment "Hex in the City", a helicopter crashes into Moe's Tavern, crushing Lenny and Carl to death. Then in 2013, it happened in real life when a helicopter crashed into The Clutha, a bar in Glasgow, killing ten people.
"Trash of the Titans": Viewed today (and ignoring the fact that this was the episode that had Homer as a full-blown jerkass), the episode seems like a satire about the rise of the Tea Party, as Homer goes around spewing angry rhetoric at a respected politician with little thought about how he'd do better if elected. Ray Patterson's lines "Nobody wants to hear the nonsensical ravings of a loudmouthed malcontent!" and "Simpson, the American people have never tolerated incompetence from its elected officials." hit harder than ever in light of how badly-received the Tea Party-dominated US Congress has been, receiving the lowest approval rating of all time in 2013.
"Homer To the Max" featured a bit at the beginning of the episode poking fun at a pay dispute between Fox and the show's cast, during which Ned Flanders walks up and comments that voice actors can be replaced and the change would be indistinguishable. As part of the gag, Ned's voice was provided by Karl Wiedergott rather than his regular actor, Harry Shearer. Shearer himself would later leave The Simpsons before production on its 27th season began (Though he would return soon after)
Dr. Hibbert's whole situation (by original design and Flanderization) of being the anti-Cliff Huxtable, in light of the Real Life crimes that Bill Cosby has done, even during the filming of said show. Especially in "On a Clear Day I Can't See My Sister", where Hibbert makes a reference to dealing a sexual harassment lawsuit.
In the South Park episode "Cartman Joins NAMBLA", the boys are playing "Investigative Reports With Bill Curtis," a Life-meets-Monopoly type board game in which players have to guess whether an event was denied or covered up by the U.S. government. When Kyle gives Cartman a jail-time card in the game, Cartman retaliates by giving him an AIDS card. The other characters are horrified by this. In the episode "Tonsil Trouble" (which aired eight years later), Cartman literally infects Kyle with AIDS thanks to a blood mishap.
The episode "Jared Has Aides" is about Jared Fogel (the famous former spokesman for Subway) telling everyone that he has aides. Hilarity Ensues (sorta). Fogel would later be jailed for child pornography and soliciting underage escorts. Then again, given that this is South Park, this could be a bit humorous to some (or will be in 22.3 years).
The G.I. Joe episode titled "Cobra Quake" involves G.I. Joe trying to stop Cobra from causing an artificially created earthquake to destroy Tokyo. In 2011, an 9.0 magnitude earthquake actually hit Japan. Because of this, The Hub suspended airing this episode on its channel until further notice.
In the episode The Legend of the Gobblewonker of Gravity Falls, Park Ranger McGucket ignores his crazy father Fiddleford, who makes a big show to the citizens of the town that a lake monster, the Gobblewonker, had destroyed his boat. Nobody but Dipper, Mabel, and Soos believe him. When Dipper finally manages to get a picture of the Gobblewonker, Fiddleford reveals that it was just a robot he built to get the attention of his son, who had been ignoring him. This was already sad, but now that it's been revealed that Fiddleford used to be sane but slowly went crazy wiping his own memory to un-see terrifying things, which would have happened while his son was only a small child, it's worse.
The episode "Trade Ya": Twilight Sparkle decides not to sell her books, saying that just because they don't need to be read again doesn't mean they don't possess value; they're a part of her history and what made her who she was, and were quite precious. Four episodes later in "Twilight's Kingdom", they along with the rest of the Golden Oak Library were destroyed by Tirek.
The Season 1 episode "Owl's Well than Ends Well" involved Spike having an insane fit of jealousy over Twilight seemingly replacing him with an owl, cumulating in him running away because he felt she didn't love him anymore. The Season 3 premiere "The Crystal Empire" puts his actions in a new light, as we find out that Twilight no longer needing him is Spike's worst fear.
Season 1's "Griffon the Brush-Off" ended with Gilda ditching Rainbow Dash as her friend. Four seasons later, the events of the episode is re-explored, and we learn that griffons literally have no concept of friendship, putting everything involving Gilda in a much different light. Rainbow Dash is the only friend she's ever had, and she has little idea how to reconcile that with Rainbow having other friends. They become friends again in the end of the episode.
In Season 1's "Look Before You Sleep", Twilight says that she's never had a sleepover before and calls out Applejack and Rarity when their bickering almost ruins her first slumber party. The Season 5 episode "Amending Fences" puts the whole episode in a different perspective when we see that Twilight had friends in Canterlot and her context implies that she never had a sleepover with any of them. It becomes even worse when we see that Twilight leaving Canterlot left an emotional scar on her old friend Moondancer.
In the season one episode "Call of the Cutie", Scootaloo tells Diamond Tiara she's 'stuck being stuck up' as a Shut Up, Hannibal!. We find out much later that she's literally stuck, as her mother was browbeating and emotionally abusing her to be a stuck up Rich Bitch like her.
Little Rosey was one among many Celebrity Toons and Spin-Off Babies featuring a no doubt slightly unrealistic portrayal of Roseanne's childhood. Considering her later incest allegations and the fact that the character Buddy was based on Tom Arnold and the ugly, bitter end to their marriage, it's best to pretend this never happened — and not because it was a bad cartoon.
American Dad!: Several episodes focuses on Francine trying to have a more exciting life, ranging from her performing surgery to becoming a deep-sea explorer. In "National Treasure 4: Baby Franny: She's Doing Well: The Hole Story", it was revealed that a firefighter seemingly died while saving her from a well, and Francine has been wracked with guilt due to feeling that she's wasted her life away and that her savior died in vain. All those attempts to make her life more exciting now have a much more tragic meaning.
In Steven Universe, one of the few times Steven snaps is when he yells at Lars for insulting his mom. "What do you know about my mom? I didn't even know my mom!" Fast forward to Rose's Scabbard and Pearl, in the midst of a breakdown, throws this right back at him. "What do you know? You've never even met her!" The similar wording especially makes the first instance so much harder to watch.
"On The Run" makes many of the events regarding Amethyst much more bitter.
The second season of Avengers Assemble "The Arsenal" featured Stephen Collins as Howard Stark. The episode aired around the time TMZ leaked an audio recording of Collins admitting to now ex-wife Faye Grant that he had molested several underage children decades before.
The interactions of Joker and Penguin inside Penguin's night club, The Iceberg Lounge, in "Joker's Millions" become this in one of the "Arkham Stories" during Batman: Arkham City.
Just try watching "Over the Edge" after Batman: Arkham Knight, and knowing what was All a Dream in the episode is reality in the game and the Grand Finale of the Arkham series. While Barbara Gordon's death still turns out to be a hallucinationnote Barbara's fear being what'd come about after she died; Batman fearing he failed to save her, the rest really happens: not only is the Scarecrow the villain, Commissioner Gordon has a What the Hell, Hero? moment towards Batman after finding about Barbara's double life, Bruce Wayne is outed as Batman, and it ends with Bruce possibly dead.
In "Make 'Em Laugh" the Joker uses microchips to alter the minds of innocents to make them criminals. ThencomesRotJ.
In the episode "Be A Clown", Mayor Hill's son Jordan is kidnapped by a disguised Joker and tricked into performing criminal acts against Batman. Jordan is horrified when he finds out. In Return of the Joker, the Tim Drake Robin is manipulated by the Joker via Mind Rape into becoming Joker Jr., later taking on the role after he unwittingly kills the Joker in a freak accident; and causes chaos in Gotham in the years that followed.
Another episode worsened by Batman Beyond: Return of the Joker is "I Am the Night", where Batman angsts over the possibility of his friends and allies being hurt...including Robin (at the time of the episode, Robin is Dick and not Tim, but still).
Yet another one episode worsened by Batman Beyond: Return of the Joker is "Joker's Favor". Charlie Collin's Heroic Heelization Speech is horribly right, because Batman will not be the one who brings out Joker's demise.:
Charlie Collins:... I found this blown out of the van. (reveals a Joker bomb) This is how it ends, Joker. No big schemes. No grand fight to the finish with the Dark Knight. Kinda funny. Ironic, really." Looks like Tim destroyed a man's dream.
Batman's origin story in this continuity (as well as others), as of July 20, 2012. In this continuity, Batman's parents were murdered by a thug (implied to be Joe Chill, but he was never named) shortly after seeing a film. The film he saw? Gray Ghost, which was the in-universe inspiration for that continuity's Batman. Flash forward to July 20, 2012, several people were killed by a madman in a shooting at a Century theater in Aurora, Colorado. The movie that was being shown on that date? A midnight showing of The Dark Knight Rises.
In "Paging The Crime Doctor", Rupert Thorne needs heart surgery. His actor, John Vernon, died in 2005 of complications from heart surgery.
In "The Laughing Fish", The Joker tries to have his Joker Fish copyrighted, and the patent guy tells him he can't copyright food. Twenty years later, Monsanto wants to do just that.
Meta example from "I Am The Night" - Batman laments the fact he's merchandised to death, on t-shirts and action figures, despite his intent. Not only was the cartoon used to sell a toy line, but not long after Warner began a massive ad campaign to push Batman toys, shirts, and other merchandise onto children.
A lot of Over the Garden Wall. Wirt blames his brother for getting them lost because he feels that Greg's antics are what caused them to fall into the pond where they're both currently drowning. He eventually gives up on attempting to get home and lies down on the ground to sleep, i.e. loses the will to live.
The Adventures of Sonic the Hedgehog episode "Mass Transit Trouble", an episode banned after the Oklahoma City bombing and 9/11 due to its plot of Robotnik plotting to bomb an airport and a subway station, becomes even more uncomfortable to watch in the wake of the ISIS attacks on Brussels Airport and a nearby subway station.
Season 4 of Ultimate Spider-Man features a lot of heartwarming moments with the Scarlet Spider where he learns to trust others and open up to Peter, his friends, and Aunt May—which became a lot less so in with "The New Sinister 6, Part 1", where it was revealed that he was really The Mole for Doctor Octopus, meaning those moments were really him playing Peter to make his betrayal hurt worse.
The Transformers Rescue Bots episode "Tip of the Iceberg"contained what happened to be a heartwarming moment when Dr. Morocco handed the Burns family a painting of Chief Burns's grandfather. "Changes" revealed that that he didn't do it out of any kindness, but as a way to sneak in a spy camera so he could spy on the family and the Rescue Bots.