One chapter has an image of a man taking a bite out of an Anpanman caricature. Takashi Yanase, the creator of Anpanman, passed away during the same week that this chapter was published in Shonen Jump.
Starting with Chapter 112, all those jokes about Nagisa's girlishness suddenly became a lot less funny with the reveal that his mother is very emotionally abusive towards him and wishes he was born a girl. This extends to things like forcing him not to cut his hair.
Much of the humor involving Kayano concerns her chest, even once being labelled "Forever Flat". In Chapter 173, "Number Two" makes it so she really has nothing in that area (fortunately, Koro-sensei was able to save her).
In one of the first-season episodes of Yu-Gi-Oh! GX, much fun is made of so-called "card crushes", Perverse Sexual Lust of a duelist towards a Duel Monsters card. Then came Yubel in Season 3.
Yu Gi Oh ARCV has a ton of foreshadowing. For example, when a mysterious boy shows up in town and meets Yuzu, Sora jokingly tells the protagonist that if he's not careful, another guy might come and steal her from him. As it turns out, Academia has kidnapped before and was going to do the same to her.
Possibly unintentional, but Mieru accidentally telegraphs elements of the final act. When Yuya is in a coma, he wears gray pajamas. Mieru is against this, as it's bad luck.She instead suggests green and white pajamas, as green detoxifies and white purifies. Come the finale, a Zarc-possessed Yuya has sickly gray skin. Zarc himself has green and white hair, but he's a corrupting and toxic force.
In Demon Slayer: Kimetsu no Yaiba, Zenitsu comically throws a long rant about how Tanjiro and Inosuke shouldnt dare to feel broken over taking part in such a grueling training for demon slayers, during their first stay in the Butterfly Estate, because according to Zenitsu being trained by cute girls is the only thing that matters, and that will always be good regardless of how tough the training is, Zenitsu tells them to commit seppuku for acting like that. Much later in the series a seppuku becomes one of the biggest tragedies in Zenitsus life, for his beloved master Jigoro commits said ritual suicide in order to repent for his other disciple, Kaigaku, betraying the demon slayers only to become a demon himself.
In one chapter of Gravitation, after Shuichi and Hiro get into a fight at school, Shuichi goes to Yuki's house to get cleaned up so his mom wouldn't see him all bloody. Yuki jokingly asks if Shuichi got gangbanged in gym class. A few chapters later, Shuichi actually does get gang raped.
Perhaps an even bigger and worse one is much of volume 9 in the manga. Volume 9 is about Shuichi being Shanghaied to New York to perform for a new record label. During one of the last major climaxes, as Shuichi and company flee from his new boss, Reiji, in order to return to Japan, part of New York City gets the ever-loving crap blown out of it. Later, though it's on a plane headed for Japan, hi-jinks once again ensue, including K busting into the cockpit and shooting (with non-lethal rounds) and bounding the pilots and taking control of the plane. Volume 9 was released in Japan on January 2000, over a year before 9/11. This is made even more jarring when the reader is treated to a nice shot of the New York skyline, which includes the World Trade Center, when Shuichi first arrives to New York City.
An early episode features a wild Tarzan-type boy who, as we see in a flashback, was lost when he was dangled out of a helicopter and then dropped. This was Played for Laughs.
In the episode "Go West Young Meowth"", when the heroes and Team Rocket visit Hollywood, it turns out to be quite run down and implied to have a large amount of poverty. Keep in mind that this episode aired about 11 to 12 years before the California Bankruptcy.
The events of the ending of "Battle aboard the St. Anne" and the beginning of "Pokemon Shipwrecked" have the St. Anne sinking, the captain making the morally dubious decision of leaving the passengers on the boat to sink (and this was Played for Laughs), as well as the believed deaths of Ash, Misty, Brock, Jessie, and James. These events end up becoming significantly harsher for Italian fans recently, when the Costa Concordia sinks off the coast of Italy in a very similar manner to the St. Anne, not to mention five confirmed deaths onboard the ship as well as the arrest of the captain for its sinking. It's unknown if this will affect their being reaired by reruns.
Similar to the above, the Battle Subway two-parter in Best Wishes consisting of "Crisis From The Underground Up" and "Battle for the Underground" will be uncomfortable for Belorussian audiences after the events of the April 2011 Minsk Metro bombing.
Then there's the dub of "Ghost of Maiden's Peak", which has James (who has a British accent in the dub) whining "I don't want to go!" as he's pulled into Gastly's clutches. Then came The Tenth Doctor'sregeneration.
Episode N featured a filler episode about a rescue team that is called in to fight a factory fire that trapped a class of schoolchildren and their teachers, which Team Rocket uses as a distraction to try to steal Pikachu. In April 2013, a factory exploded in Texas and the Boston Marathon was bombed, with one of the victims in the latter case being an 8-year-old boy.
XY The Series had one in a planned undersea episode centered around Skrelp and Dragalge; which was pulled from its initial airing and replaced with Ash's gym battle with Grant after the sinking of a South Korean ferry.
The Sun and Moon series has a Running Gag involving the character of Lillie being afraid of touching Pokémon, which she is attending the Pokémon Academy to help overcome; and gets better with over the course of the series. Episode 47 reveals what led to this fear: an accident when she was younger involving the Ultra Beast Nihilego, which she has repressed memories of. As a result, the gag becomes much less funny and Lillie's fear; as well as her desire to overcome it are much more understandable. This is furthered in episode 49 which reveals that Faba was responsible for bringing Nihilego from Ultra Space and trying to keep Lillie from rediscovering the truth, further compounding the desire for Lillie to overcome her fear with the help of her friends.
One of the longest-running jokes about the series is Ash's Pikachu not wanting to go into his Poké Ball. This becomes much darker after Pokémon: I Choose You! where Ash successfully got Pikachu into his Poké Ball to save him from being obliterated by attacks of a bunch of Brainwashed and Crazy Pokémon in a Heroic Sacrifice.
In Pokémon: The Power of Us, a Running Gag in the movie is the character of Harriet not liking the company of Pokémon, until the final act of the film reveals that this stems from losing her Snubbull in a fire 50 years prior to the events of the film.
Prior to 2017, Disney handled the North American distribution of most Studio Ghibli movies. When it came time to dub Princess Mononoke , Disney chose to make it under the banner of its then subsidiary Miramax Films (led by Harvey & Bob Weinstein) due to its violence. The Weinsteins had quite the reputation for chopping up movies in the editing process and they wanted to cut the movie down to PG from PG-13 to market it to kids. Director Hayao Miyazaki and his team wouldnt be bullied and stood by keeping the film as is. Miyazaki also went to New York to talk to the brothers about it and told The Guardian in 2005 that he was shocked at how aggressive Harvey was to him. Having been burned once before by overzealous editing, Studio Ghibli also had made sure that having final say over what got edited out was written into the contract with Disney. Legally, there was nothing Miramax could do. It culminated in one of the producers sending a real katana to the Miramax office with a note attached saying No cuts!. In the same interview, Miyazaki laughed about coming up with a clever way to best such a bully. This funny way of dealing with him isnt so funny anymore after it came to light that Harvey was using his aggression and power not only to try to berate a man who doesnt even speak fluent English into editing his movie but also to ruin countless numbers of womens careers for not sleeping with him.
Also, in Princess Tutu, Mike Kleinhenz plays the villainous Raven, and what is the one thing he desires? A heart.
Also in One Piece, Luffy finds Bon Clay in Impel Down, and is overjoyed to find him alive after the last time he saw him getting blown up luring marines off the Strawhat's trail. Bon-chan laughs at him, and says "Okamas can never die!" And then of course, he repeats his self sacrifice with someone a little more sinister than Hina. Though of course, this being One Piece, and the act happening off screen, he's later revealed to have survived.
Ace's boss, Whitebeard, is a walking Moment of Awesome. His Devil Fruit ability? The power to make earthquakes. Wouldn't be so bad if he didn't also use this ability to flood an island with a tsunami. It gets hard to watch his Awesome Moments after the 2011 Tohoku earthquake and tsunami.
Several of the main characters' traits, such as Usopp's lying, Nami's obsession with money, and even Brook's eccentric nature are used for comic effect. However, each crew member eventually gets a flashback, many of which reveal tragic origins for these traits. For the most part, though, this doesn't stop them from being funny afterwards.
A couple jokes are made by Usopp about people using scrapped ships: once during a filler episode regarding Fullbody, and again as the Skypiea arc begins regarding Mashira. It takes on a darker turn in Water 7 when the Going Merry is damaged beyond repair and Usopp is unwilling to let it go.
While the reveal of Señor Pink (a grown man dressed like a baby, complete with pacifier) is initially hilarious, it becomes far less so when it is revealed that he wears these clothes in memory of his dead son, and also to make his catatonic wife smile again. DAMN.
Japanese television personality note (and ex-pornstar) Ai Iijima was given her own manga series, titled Time Traveller Ai. One arc of the three-volume manga had Ai visiting a dystopic Waterworld-type future, where she met a descendant of hers. Iijima was found dead of pneumonia on December 24th, 2008. She had died alone, and unmarried.
The ending of Mobile Suit Gundam 0083: Stardust Memory. A terrorist attack decimates North America due to interference from a militarist faction within the government, who then use the attack as a justification to expand their influence & start another war. And this was made in the early 1990s!
One of the Running Gags is that, as the icing on the post-apocalyptic cake, America's going through a recession. To boot, one of the SEELE boardmembers says off-handedly, with (to Americans) alarming nonchalance in a conversation in the TV series, "The United States seems to be 'allergic' to unemployment, but they'll learn." Shudder.
In episode 7, a prototype mech touted as being more reliable than the Evangelions is being extravagantly unveiled for its first ever activation, to which several people, including the press, and two of NERV's highest ranking employees (namely Ritsuko and Misato) are invited. Dr. Akagi voices concern that its power-supply is a solid-fueled nuclear reactor, and the dangers that a core meltdown would pose. Of course, that's exactly what happens, and it's up to Misato (with help from Shinji & Unit 1) to prevent the runaway mech from suffering a runaway reactor meltdown. Made for exciting action, until the disaster at Fukushima Daiichi.
Misato joking to Ritsuko in one of the first episodes that she's "not going to put the moves on Shinji". This has been nicknamed the "irony bomb" by parts of the fandom.
The scene where Shinji compliments Rei by saying she would make a good mother definitely qualifies, once you find out that Rei is a partial clone of his mother. The scene isn't helped by Rei's nervous expression and blush in response to the compliment. On the first viewing, it looks like she's just being cutely awkward. Once you know the whole truth about Rei, it seems more like she's nervous because Shinji is getting way too close to the truth.
At one point, Rei says that all she is, is a pilot; and if she stops piloting Eva, she'll cease to exist.
Spike Spencer's rant on the NGE Platinum DVD. "Uuuhh... Is this how you end a series? I mean, is this... Where we go from here? Okay, the movie better sure as hell make up for this, I'm telling you, 'cause I'm stuck in nowhere land".
Adam sent Earth off its axis, much like the Sendai earthquake.
Simoun: When Chor Tempest gets asked to show a Plumbum priestess around their ship they naturally start off with introductions, with the priestess repeating each name as she's told it. All except Aer's. A funny little snub, right? Not so funny when it's revealed why she won't say "Aer". Until she does, anyway.
There are also episodes about Russia. In one of them, he introduces his sister Ukraine and explains his difficult relationship to her, and another one is about the G8, with England expressing that he thinks Russia shouldn't be a member anymore. Now, Russia is suspended from the G8 because of the way the countries politicans behaved during the Crimean crisis, and there's a civil war in Ukraine over the question wether the country should rely more on Russia or more on the EU in terms of economy.
Nerima Daikon Brothers has a parody of Michael Jackson as an end-of-series villain, complete with the usual jokes. It isn't really that bad to anyone who isn't that sensitive to the his whole being dead thing, at least until the line "You're right, I DO look like Sammy Davis Jr.! Well, except for the being dead part".
In episode 6 of Peacemaker Kurogane, Nagakura Shinpachi accuses Vice-captain Yamanami of cheating during a footrace by turning abaci into rollerskates, and demands (jokingly) that he commit seppuku. Yamanami is Doomed by History to end his Shinsengumi career by committing seppuku.
Similarly, in an early episode of the anime, Okita walks in on Hijikata making medicine, and jokingly states that no one will have to worry about catching colds. Okita will later die of tuberculosis.
As an In-Universe example, Joseph fakes getting his hand cut off when Santana tries to absorb him. Later on, Kars chops off Joseph's hand for real.
In the Azumanga Daioh supplementary lessons, Osaka believes she is going to have a good day because she woke up early, only for an earthquake to rock the school moments later. Keep in mind, the school they go to is in Tokyo. Yeah, joke no longer funny.
It's mentioned in Shaman King that American Indian art is popular in Japan. A group of Navajo artists are raising money to help victims of the tsunami.
And then we have Ishihara's comment about Japanese culture being too materialistic and that causing the earthquake. Shaman King makes this a personal hobby horse.
Many consider Hiroe's diatribe completely unfunny—Kon's condition was public knowledge (as Kon blogged about his condition until his death), so the remark looked as if Hiroe was speaking ill of Kon.
Part 6 of Hentai manga Secret Plot Deep involves the main characters going to a beach north of Tokyo which is deserted due to everyone's worries about the nearby nuclear power plant. Gyaa.
Dragon Ball had Goku being nicknamed by his friends as "monkey-boy" in reference to his monkey-like tail. With Dragon Ball Z, however, and the frequent use of the term "Monkey" towards Goku and the other Saiyans by Frieza and his men, his friend's nickname for Goku comes off as awfully racist in retrospect.
In the opening shot◊ of Blassreiter episode 2 one of the headlines in the (German language) newspaper reads "Knut the polar bear becomes daddy". It was a fun little background detail at the time, but unfortunately Knut died in 2011. And to make things really tragically ironic, he was castrated about a year after Blassreiter came out.
Fighting Foodons: Episode 15 has some townspeople afflicted with "swine flu" after coming in contact with lettuce pigs. This lost all humor after the H1N1 outbreak in 2009. Also qualifies as Harsher in Hindsight due to many cases of the disease being contracted from underprocessed pork products.
In episode 3, Usagi talks about how much fun it must be to never wake up again, because you get to stay in your dreams forever. It wasn't so much fun in episode 69, when she almost died because she couldn't wake up. Or in Super S: The Movie , where she forcefully wakes herself up from what could've been an eternal slumber, despite the fact that she was having wonderful dreams involving Momoru
In episode 145, Fisheye attacks and tries to kill a young ballet master simply because he wouldn't give him the role of Giselle. While this is one of the more light-hearted examples of Disproportionate Retribution (this being SuperS), it suddenly became one of the darkest moments in the most lighthearted season of the anime after Bolshoi Ballet artistic director Sergei Filin got splashed in the face with acid on January 17, 2013, in one of the most horrific incidents in the history of the Bolshoi Ballet, particularly as far as the infamous in-fighting and rivalries are concerned.
In the Area 88 manga, Saki's female bodyguards were a lighthearted nod to Gaddafi's Amazonian Guard. The arrangement seems a lot less sexy now that members of the real-life Amazonian Guard have accused Gaddafi and his sons of sexually assaulting them.
The backstory of Jinmenken/ Manjimutt in episode 3 is that his freak accident that led to him becoming a yokai stemmed from being let go from his job as a salaryman due to budget cuts. Two years after the episode first aired in the US, the exact same thing happened to the cast of the English dub.
Sgt. Frog: "Keroro Killed the Radio Star" had one character worriedly comment that their radio show ratings were "dropping faster than an Amy Winehouse song". Funny Take That! then, not so much since July 2011.
A minor one that's related to the Kyoto Animation arson: one of the jokes in the second episode of Nyoron Churuya-san involves a fire evacuation drill, with the punchline being that Churuya-san gets left behind. It's hard not to feel a lot sadder when she says her Catchphrase after the real-life tragedy.
In Baccano!, members of the Martillo family find much amusement in the fact that Firo manages to remain a virgin into his nineties (especially since he's been married for over twenty years). Then Another Junk Railroad featured a conversation between Firo and a concerned Berga that heavily implies that Firo has a Paralyzing Fear of Sexuality because he was almost raped when he was younger.
An episode of Rozen Maiden Traumend has Kanaria refer to the doll Barasuishou as "Bara-Bara". In Japanese, the word "barabara" means "dismemberment/breaking apart". Barasuishou's body collapses horrifyingly in the last episode.
In Fullmetal Alchemist, it's pretty hilarious whenever Hughes shoves pictures of Elysia and Gracia in other people's faces and rants about how adorable/beautiful they are. The aneurysm comes when Hughes can't bring himself to shoot Envy due to the homunculus pulling off a Shapeshifter Guilt Trip via turning into Gracia and murdering him, still looking like his beloved wife, having copied her appearance from a picture he dropped.
In the Fullmetal Alchemist anime, Hughes tells Mustang to hurry up and become a brigadier general, to which Mustang replies, "that's easy for you to say". Hughes, formerly ranked below Mustang so that he could support his friend from below, gains two ranks and becomes a brigadier general after he is killed.
A Running Gag in the series is Mustang being rendered useless by rain (or getting wet in general) since he can't create flames with wet gloves. Hawkeye doesn't hesitate to remind him of that he is "useless when it's raining" whenever it happens. In the aftermath of Hughes' funeral, he bitterly comments, "It's raining..."
An In-Universe example: when Ed first fought Envy, he complained about his Shapeshifting; then Envy taunts him by asking if he would prefer him to look like a taller version of Ed. During the penultimate episode, Envy finally revealed his true form; instead of being the expected One-Winged Angel, he looks like a taller version of Ed. He's Ed's half-brother, the son of Ed's father Hohenheim and the Big Bad Dante.
Also, during a flashback of the Ishval conflict, Mustang jokingly tells Hughes that the soldiers who never stop talking about their girlfriends back home always end up dying. You've probably figured out what happens to Hughes by now.
An early chapter of the Magical Girl Lyrical Nanoha A'smanga had a scene of a sweatdropping Chrono asking Yuuno, "Won't it be too much for (Nanoha) if she continues like this?" in regards to Nanoha's Training from Hell, a cute Lampshade Hanging of the main character's completely over-the-top training method that became hauntingly prophetic in the following season when Nanoha almost got killed and became hospitalized for nearly a year mostly because she overextended herself.
Not the only time Nanoha's pushed herself way too hard - her overuse of massively boosted magical energy at the end of StrikerS damaged her actual magic potential, specified directly in the Sound Stages. It's why she's off combat duty in Magical Girl Lyrical Nanoha ViVid, four years later.
In the "Freaky Friday" Flip episode of Revolutionary Girl Utena, Utena jokes about wanting to get out of Anthy's body before she gets caught up in some weird ritual sacrifice. Neither she nor the audience knows then that the whole Rose Bride thing works a lot like that.
Another example: near the end of both anime series, Negi forms a Pactio with all the members of his class. This sounds funny until you realize that this includes Chao Lingshen, who is revealed later in the manga to be Negi's distant descendant.
Another In-Universe example, Chao Lingshen's Real Identity IS AN ALIEN FROM MARS!! Jump to the Magical World arc: The Layout of the Magical World is similar to the planet Mars. That "joke" that Chao made earlier really IS a Cassandra Truth AND you later find out about Chao's future timeline and HOW BAD IT REALLY IS yet as a student she still tries to always keep a smile on her face.
In a similar vein, there is an enormous amount of Ship Tease between Negi and Asuna over the course of the entire series. Then we get to chapter 252 and the apparent confirmation that she's his aunt.
This particular aneurysm has proven potentially survivable with Chapter 284, which reveals that Asuna is an Artificial Human and Really 700 Years Old - two things that make her being his aunt impossible.
A rather more disturbing one: early on, Negi accidentally erasing Chisame'sPlayboy Bunny suit from existence by turning it into flower petals". Then, much later on, the exact same thing happens to a person.
Right before going to Magic World, during a sparing between Evangeline and Negi/Asuna team, Asuna manages to cut Eva's cheek, and gets frozen solid in return, and then in chapter 284 we see that in her past she was sealed in some kind of crystal.
Asuna wakes up early for her job, but whenever she can, she sleeps well into the day and is quite a heavy sleeper. A hundred chapters or so later, she is put to sleep for another hundred years for Negis plan to save the world, meaning she won't see everyone for a hundred years. Not many people survive to live until they are 115, but Ayaka did. And then Asuna oversleeps by 30 years.
Back in chapter 249, Rakan made an off-hand remark how little Negi resembles a main character, telling him he's more akin to the side character that dies 3 chapters before the ending. In the timeline Asuna slept 130 years through, set in chapter 352 of a 355-chapter series, this is accurate.
One of the penultimate festival episodes had Viletta being forced to participate in a swimsuit competition; to which she jokingly retorts that she'll "kill Shirley 100 times over" for making her do it. Much less amusing later on in the series when Shirley is Killed Off for Real.
In Valvrave the Liberator, Haruto has several Accidental Pervert moments with Takahi - accidentally getting part of his monster costume under her skirt, for instance. Then his Horror Hunger starts to take over when he's in an elevator with her, but Saki - who knows about his curse - shows up to stop him just in time. And then, well... he needs Runes, "the building blocks of information", and apparently human pain is a good source of them. So Rape as Drama ensues, with Saki as the victim, just after the elevator incident.
All of the silly almost-confession and Not What It Looks Like moments at the shrine near the school - which is where the aforementioned Horror Hunger attack takes place. Lampshaded when they finally return to the module in the end of season 2, when Haruto is being interviewed there by a TV reporter, and he looks back at all of the horrific incidents that the people idolizing them know nothing about. And then things go From Bad to Worse...
In episode 7 of Kamigami no Asobi, Baldr tells Yui that because of the vow his mother made with all of nature, nothing can hurt him... "But I can hurt myself, if I trip and fall." In the end of episode 11, he jumps off a cliff in a suicide attempt so that Loki, who loves him, won't have to kill him to stop his Superpowered Evil Side.
Early on in the ×××HOLiC manga, Yuuko dramatically pretends to be dead from the heat, and Maru and Moro even set up a fake crime scene investigation. This becomes much less funny when it's revealed that she's been Dead All Along.
Also, a critic commented that Yuuko looked like "a sexy zombie" when she appeared on the covers of one of the DVD box set. This, likewise, is not as funny as it once was when one takes into consideration that she was dead at the time.
In Challengers, Souichi is violently homophobic after an incident several years before where a professor tried to rape him, only to be narrowly saved by Morinaga. When Morinaga finally comes out of the closet to Souichi and confesses his own love, Souichi manages to get over his homophobia enough to keep Morinaga around as a friend and lab assistant, and Morinaga proudly tells another friend later that he's "proven that not all homosexuals are Satan's rape demons." Cue spin-off manga The Tyrant Falls in Love, where the overarching conflict is set up by Morinaga taking advantage of a drugged but very aware Souichi.
The opening theme to DearS is, essentially, a love song entitled "Love Slave," and one of the repeating lines in it is, in Gratuitous English, "I'm Your Slave". Then you get a good portion of the way into the series, and you find out that the aliens of the title are a purpose-made slave race.
Tengen Toppa Gurren Lagann has one in episode 5.5 (a special OVA bundled with any preorders of the Nintendo DS game). In one scene, Kamina is hurled off a cliff only to be shown immediately holding on for dear life. He then remarks "whew, I almost died." If you've seen the whole series, you know the problem.
In episode 12 of the first season of Mobile Suit Gundam 00, Louise Halevy is disturbed by the fact that her mother says how Saji reminds her of her husband (describing how Saji looks like her 'husband reborn'), with Louise citing that he is still alive. It is a lot harder to watch after episode 18, when her entire family is killed by Nena Trinity during a wedding.
In episode 11 of AIR, Haruko makes up for not spending time with Misuzu and they agree to start over. The next day, Misuzu loses her memories (as per the prophecy Yukito was told) and Haruko has to build their relationship back up from the beginning.
In-universe example: In Wolf's Rain, the boys get stuck in a storm and Hige and Toboe start complaining about the lack of food. Tsume jokes that they "can start with the runt, since he's weak, and then eat porky." Then, in the second to last episode, Tsume has to use his teeth to tear out Hige's throat in a mercy kill. This line may also offer a bit of Hilarious in Hindsight, no pun intended, given Tsume and Toboe's later interactions.Which takes it right back into Funny Aneurysm territory with Tsume's reaction to Toboe's death.
Halfway thought the first episode of Higurashi: When They Cry freelance photographer Tomitake asks Keiichi what his friend, Rena, is doing in the garbage dump. Keiichi makes a crack about her "going to check a body that she killed". While it was barely received as a joke at first, it eventually gets even more awkward and disturbing.
Fridge Brilliance occurs later on in the answer arc, where she does kill two people, keep them in the dump, and goes to check on them often as her mental status deteriorates.
In a more light-hearted scene we watch Mion joke about her "evil" twin sister and are shown an Imagine Spot with a chibi Shion beating a chibi Mion with a whip. The Imagine Spot wasn't so funny when we see Shion beating her own grandmother with a whip later on.
"I like using poison to kill because it's a gentle death" becomes a lot less funny when (in Meakashi-hen) Rika is injected with the cure for the Hinamizawa disease that she'd intended to use on someone else, which gave her an allergic reaction since she is the carrier, leading to her being weakened and committing suicide so she wouldnt be tortured to death.
Monster: When Nina first receives the romantic-sounding email from the man "born to smother her with flowers," she laughs at it as a perceived attempt of her Butt-Monkey friend to seduce her. When, in retrospect, it is revealed that the sender is her own brother, the romantic subtext initially seen becomes truly cringe-worthy.
In the manga of Fushigi Yuugi (volume 2), Miaka regains consciousness after stabbing herself to save her warriors from the Evil Miaka demon-thing. Nuriko teases her by saying, "I never thought for a second that a stupid, overly optimistic food monger like you would die!" Miaka counters with, "Oh, shrivel and die, Nuriko!" It's actually quite amusing until you read volume 8/watch episode 33, when Nuriko does indeed die.
In the early episodes of Nana, Nana Komatsu gets paranoid about her boyfriend, Shouji, cheating on her for a girl named Sachiko, complete with exaggeration that makes it hard to take her seriously. Guess what happens a few episodes later for real.
Star★Twinkle Pretty Cure: Hikaru's complaint about Earth getting hot is this (not to mention Unintentional Period Piece) due to the heat wave in Europe that began the day after the ep premiered. (Due to time zone, tonight in Europe is tomorrow morning in Japan).
In Bakuman。, the strain of working on manga while in school is not portrayed completely seriously at first, with the characters falling asleep in class to catch up on sleep. Later on, though, Mashiro gets hospitalized for pushing himself too far.
Fukuda once notes that Nakai "looks like a stalker" when drawing outside Aoki's house so they can team up again, but the scene is played as proof of his Determinator nature. Later on, Nakai essentially tells Aoki that she can only work with him if she becomes his girlfriend, thus suggesting that he was selfish and emotionally manipulative back then.
Soul Eater: the scene in Justin's debut where both Spirit and Yumi kick him in the back for having his earphones in when Shinigami is talking (his lip-reading is useless when Shinigami has no visible mouth). We later discover where Justin's allegiance (apparently) truly lies, and that he was, therefore, never listening to Shinigami. Come to think of it, that also casts the scene where Shinigami gets Spirit to 'translate' - "Repeat after me!" - in a different light. Although it could easily be Shinigami being Shinigami.
Death The Kid's Super OCD is Played for Laughs usually and his freak-outs are pretty funny. That is, until the Book Of Eibon arc in the manga in which he goes mad and wants to destroy all of existence to create perfect symmetry via nothingness. Luckily, Black Star snaps him out of it, but his obsessive nature isn't quite as funny since then.
Meme's main schtick in Soul Eater Not! is her tendency to forget things, including her own name. This gets a little bit darker when she loses track of a whole day, and then a lot darker when she turns out to be one of Shaula's People Puppets. The memory loss is discussed as a possible side effect of the drugs and magic that Shaula uses in her mind control spell. Suddenly, seeing Meme tie her hair the wrong way isn't quite as funny anymore.
In Nisemonogatari, Kanbaru makes an offhand comment about how Sengoku Nadeko is the "Final Last Boss" due to her Moe traits and the hook she's planted into lolicon Araragi's mind. Five novels later in Otorimonogatari, Nadeko has awakened her Superpowered Evil Side due to her repressed Yandere tendencies for Araragi and as of that novel is an enemy of Araragi, Shinobu and Senjougahara. Aptly, the story is entitled "Nadeko Medusa", for her oddity's form is of a medusa.
Interestingly, this plot thread may have been born when Nadeko's voice actress, Kana Hanazawa said in an interview with Nisio Isin that she had always wanted to voice an evil character.
Kazuko's inserting rants about her failures to get a boyfriend and the difficulties associated with her age into her lessons is meant to come off as funny at first, but once you consider Sayaka crossing the Despair Event Horizon primarily due to being unable to get together with Kyosuke, what Kazuko is going through comes across as a potentially very emotionally damaging experience, and one has to wonder about her well-being. Her raving in Rebellion about the Mayan apocalypse and wanting the world to end because she can't get a stable boyfriend is an even cringier example, after Homura resets and heavily modifies the universe to satisfy her obsessive love for Madoka.
Sayaka teases Madoka about her Homura-related dream in the first episode, saying she must have known Homura in a previous life, and destiny has transcended spacetime to bring them together. In the manga, she jokes that they must be star-crossed lovers. All of this is essentially true, thanks to Homura's relentless time-travelling, and the details are horrendously traumatic.
Similarly, Homura is often depicted as a crazedMemetic Molester in fanart, as a joking contrast to her normally stoic demeanor and as an elevation of her devotion to Madoka into Single-Target Sexuality. Then Rebellion came along, and Homura turned out to be willing to steal Madoka's power and remake the world into a prison for her. Suddenly, the fanart depiction seems pretty kind.
In one of the specials for My-Otome, Shiho, after being left with the wrong straw and being told to hold down the fort while her fellow Trias members Akane and Chie relax during the survival exam, uses her "spiraling" to cause a massive tidal wave that washes away all the people on the beach. Naturally, this scene comes off as quite disturbing in light of the recent aforementioned tsunami.
Near the beginning of the Jinchuu Arc of Rurouni Kenshin, Enishi tells Kenshin that he has ten large battleships (of the type deployed by Shishio in the previous arc) and threatens to use them to burn Tokyo to the ground if Kenshin backs out of their upcoming confrontation. Now compare this with the infamous Buster Call from One Piece, which is virtually the same thing. It's also entirely possible that this was intentional since Eiichiro Oda, author of One Piece, used to be Watsuki's assistant before starting his own series.
Another one happens in the anime near the beginning of the Kyoto arc when Misao and Kenshin meet for the first time. Upon seeing the state of him, Misao asks if Kenshin's wife ran away from him, setting off several more funny moments. Tomoe didn't run away, but maybe whatshe did do still counts... That's a little less funny.
In Macross Frontier episode 6, after Ranka starts singing, Nanase encourages her with: "Become the next pop idol! Overthrow Sheryl!". First time this was funny, but during rewatch, this is very cringeworthy since in episode 18 said "Overthrow Sheryl!" turns out to be a totalTear Jerker for Sheryl. It doesn't turn out well for Ranka either.
One of the running gags in School-Live! involves Megumi getting ignored often by the other girls except Yuki during conversations, especially in episode 2 when they make remarks about how they're still young and don't notice her discomfort with the subject. Later in episode 6, it's revealed in a flashback that Megumi was killed while protecting the other girls from zombies. Hence, the reason why the other girls except Yuki ignore her is because she isn't there.
When fighting Lunatic, Kotetsu jokes about the palm-like design on his mask. Episode 16 informs us that it is because Yuri Petrov has a hand-shaped burn mark on his face from when he killed his father.
In My-HiME, Reito once jokes that he decided to make Shizuru come to the student council meeting instead of tending to the sick Natsuki because he "thought leaving Shizuru-san alone with Natsuki-san would be too dangerous". Later on, it turns out that Shizuru has been keeping her feelings to Natsuki to herself because many people, including Haruka and herself, find them improper, and while Natsuki is asleep, kisses her (and may have gone even further earlier). One fan comic notes that Shizuru's casual attitude and joking that she and Natsuki were "just getting to the good part" when Reito and Yuuichi walked into the student council room is a bit of a Tear Jerker considering the later revelations about how Shizuru feels about her love for Natsuki.
Penguindrum's ED, in which Himari and the Double H girls get dolled up and dance around happily becomes a lot harder to watch after Episode 9 reveals that the Double H girls used to be Himari's friends and that the ED is a wistful reminder of something that can't happen for her.
Also, seeing the beautiful Yuri in a princess-like pose and garb in the first OP is harsher when you learn how her father wanted "to make her beautiful" via using his chisel to carve up her body.
When the Princess of the Crystal refers to Shouma and Kanba as "lowlifes that never will accomplish to anything", it's really freaking funny. When little Himari refers to herself as "someone who never accomplished to anything" as she's in the Child Broiler, it's really freaking sad.
Psycho-Pass was written by the same guy as Madoka above, and also doesn't skimp on the cynical darkness. Episode 10 features a man hunting humans for sport to relieve his boredom. Much like how Madoka's pivotal Episode 10 (see above) aired the night before the Tohoku earthquake, this one aired in Japan the day before a horrific school shooting in America. The themes of mental illness and criminality in the anime do not help. That's two in a row for Urobutcher.
Ukitake's "funeral" (with him buried in a sand casket) in the Beach Episode becomes outright depressing to watch after the second-to-last chapter of the manga.
Early in the manga, flashbacks reveal a very young Uryuu asking Souken if the old-fashioned Quincy wardrobe will ever be updated because the uniform is totally uncool. In the Arrancar Arc, Uryuu announces to the Arrancar, in a very hammy scene, that Aizen should fear Quincies, not Shinigami. The final arc reveals the Quincies aren't extinct, they've conquered Hueco Mundo, are performing ethnic cleansing on the Arrancar and their uniform has changed to reflect the Nazi overtones. The Quincies then invade Soul Society, trash the city and decimate the Gotei 13 by half in only a few minutes of fighting - including wrecking several captains and lieutenants. Then Uryuu betrays his friends by joining the Quincies, Putting on the Reich himself (though this is a ploy to get close enough to assassinate their leader).
A Running Gag of Tsutomu Tanaka of Kenichi: The Mightiest Disciple is that he'll often pause in the course of the action to speak to his wife on the phone. Coming across as a Henpecked Husband despite being a genuine badass. As of an arc in which he challenges the man who killed his master, we learn that all this time he's been calling an automated Test Call every time and his family has been Dead All Along.
In Saki, Yuuki, after losing a game of mahjong in the training camp, accuses Nodoka of hiding mahjong tiles between her breasts. In the prefectural tournament arc, one of the members of the Ryuumonbuchi team, Hajime, is revealed to have cheated at mahjong in elementary school (via sleight of hand), and as a result, feels guilt and a desire to regain the trust of others, resulting in her wearing the chains on her wrists.
In a gag strip of one of the early volumes of Fruits Basket, Shigure tells the audience that Yukiis actually a girl. Then you discover that Akito really is a girl pretending to be a boy, and Shigure knew about it. Still funny, but it comes across as pretty cruel.
In Nyaruko: Crawling with Love!, Nyarko repeatedly attempts to get her Love Interest Mahiro's attention by giving him custom-made "Nyarko goods", like body pillows or a "Yes/No cushion" that depicts her wearing slinky black lingerie. She does finally wear that lingerie in the second season, but it's during a very painful emotional breakdown caused by Mahiro playing The Beard for another girl, in which Nyarko sobs that his Cannot Spit It Out attitude — quite literally, being unwilling or unable to give a definite "Yes" or "No" answer to "Do you like me?" — is driving her crazy.
When Rundelhaus in Log Horizon was first introduced, he was depicted as a Small Name, Big Ego with Leeroy Jenkins tendencies, frustrating his party members greatly even though his Large Ham made him hilarious to viewers. However, when he was later revealed to be a Person of the Landnote who, unlike player characters (Adventurers), cannot be revived upon death after being fatally wounded while protecting his comrades at arms, his past antics suddenly became much more poignant; his boasting can now be interpreted as his inability to fully comprehend the vast skill disparities between People of the Land and Adventurers and his habit of charging forward without coordinating with his party properly represents his desperateness in "becoming" an Adventurer.
Sword Art Online: In episode 8, Kirito accidentally grabs Asuna's breast when she falls on him. Cue Kirito being smacked in the face for humor effect assuming he did so intentionally. The scene wasn't so funny 16 episodes later when Asuna ends up being nearly raped. In front of Kirito.
In Fairy Tail, Natsu pretends to be the Great Demon Lord at the end of the Edolas arc to help Mystogan retain peace, and it's honestly one of the funniest moments in the manga. Much later, the final chapter of the Tartarus arc reveals Natsu is actually E.N.D., the first and most powerful of Zeref's demons, and whose full awakening will spell tragedy for everyone around him.
Part of the reason why Plastic Memories' use of comic relief is being critiqued by some viewers is because Isla is near the end of her life. As Episode 2 revealed, she only has 2000 hours left to live, meaning her antics of confused speech, diminished dexterity, and bizarre decision-making are the result of her functions slowly deteriorating. This makes some of her comical scenes from Episode 1 to be... not so funny in hindsight.
It's a Running Gag for Krista/Historia to be referred to as a "goddess" by other characters. Then her father tries to force her to inherit the power of the Founding Titan and eat Eren, which would make her a literal goddess at the expense of her humanity.
Yuki Yuna is a Hero: In Episode 2, Yuki Yuna tries to cheer up her best friend with some dried flowers. (The attempt fails hilariously.) Pressing flowers is her hobby. All the girls and their magic are represented with floral imagery and flower-inspired costumes. As they use their magic, they are afflicted with disabilities.
Ranma ½: Any scene where someone goes after Ranma's pigtail, after it's revealed that he absolutely must wear his hair that way to avoid going bald (it's a long story). Thankfully, the curse wears off eventually.
Mob Psycho 100: At the end of each episode, Reigen gives a sales pitch for the next one, in line with his personality as a con man. When Reigen is presumed dead at the end of Episode 11, Mob voices the post-credits scene instead.
Mob:Next time on Mob Psycho 100 Episode 12: 'Mob and Reigen.' This was in Master's will: Watching the finale in real time is an excellent decision.
In Made in Abyss, Ozen tells the heroes that Bondrewd is not "kind" like she is. This after she pummeled both of them to unconsciousness (supposedly to prove they weren't ready to tackle the Abyss) and then put them through a half-assed "survival training" lesson where they had to camp out for several days in the territory of an aggressive hippo-like creature. Reg incredulously asks if she's joking, and she hits him. Later on, though, you find out exactly what Bondrewd gets up to, and Ozen looks like a saint by comparison. He's a Mad Scientist who performs horrific experiments on orphaned children, turning most of them into mutated blobs. One of the blobs also becomes immortal, so he kills her repeatedly.
In an early episode of Ōban Star-Racers, Molly states that she would rather fall into a bottomless pit than listen to him (the 'him' being Don Wei). In the race directly after she and her father have a long-overdue discussion when Don reveals that he now realizes she's his daughter, Eva, the Whizzing Arrow is badly damaged and plummets down the almost bottomless canyon. Oops.
The Quintessential Quintuplets: In Chapter 21 (Episode 8 of the anime), there's a brief scene where Yotsuba tells Fuutarou that the reason she takes his side over his sisters is not because she wants better grades, but because she likes him. Then she grins evilly and says she was just joking, and the narration even plays it up by saying "In that very moment, Fuutarou's heart hardened a bit" after he says he won't trust anybody ever again. Come Chapter 90, we see that Yotsuba was not lying when she said that, and has been in love with him for years (the chapter even foreshadows it by establishing that Yotsuba is a Bad Liar).