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The Spanish slapstick comic Mortadelo y Filemón had tons of minor jokes in the background, but the most infamous is this panel of 1992 (the one showed in the Trope's main page), in which a plane is seen crashed in one of the Twin Towers.
Transmetropolitan ended with Spider Jerusalem degenerating under an incurable disease and about to end his life by putting a gun up under his chin. It was actually a cigarette lighter. As it turned out, he was fine. A few years after the end of the comics, Spider's real-life inspiration Hunter S. Thompson ended up doing pretty much the exact same thing...
52 had an early Running Gag that revolved around ReneeMontoya's cigarette habit and her mentor, Vic Sage, constantly trying to educate her about the harmful effects of smoking. At one point, she goes so far as to blow smoke in his face. Ha ha, funny joke. Then we learn that Sage is dying of lung cancer...
Not to mention Renee's line in week 14 that she swore by the end of it, she'd hold his dead body in her hands. Heck, most of Renee's early dialogue involving Charlie just reeks of this, intentionally.
There was a warmly received reunion mini-series of former JLI members featuring among others, Blue Beetle, Maxwell Lord, Elongated Man, and his wife Sue Dibny. The mini-series was so successful, the writers immediately wrote a sequel. But the artist couldn't keep up with the punishing schedule DC was trying to place on him, so the release of the sequel was delayed for a year so that DC could give us Identity Crisis instead, where Sue Dibny is murdered, burned, and autopsied, and it's also revealed that years earlier, she was raped by Dr. Light. All of which is depicted quite graphically, leaving little to the imagination. Oh, and it also turns out she was pregnant at the time of her murder. When that reunion sequel was finally released, it featured a Running Gag where everybody thinks Sue is pregnant and she angrily denies it. This gag is in Every. Single. Issue.
Given everything that's happenedtothem, Giffen's entire run of JLI could be seen as a "Funny Aneurysm" Moment. Nearly all of the members of one of the more light-hearted takes on the Justice League have suffered tragic fates.
Ultimate Marvel had a borderline example in Ultimate X-Men. After explaining to Beast the true nature of a project Nick Fury had him working on, Bishop says that Beast's work meant that Nick Fury wouldn't be executed for causing a mutant genocide. The "aneurysm" comes in the Ultimate Power miniseries, where Nick Fury is imprisoned on the Earth of the Squadron Supreme for the deaths of millions.
A deliberate example occurred during the "Rainmaker" arc of PS238... While Tyler, Zodon and Guardian Angel are sent outside during the rain on flag-duty, Zodon riffs about how Tyler's 'mere human' immune defense system surely cannot withstand the rain and is likely to cause his imminent death. A short while later, The Rainmaker temporarily neutralizes Guardian Angel's powers in order to get past her; when she then proceeds to stand out in the rain for over an hour, she catches a multitude of opportunistic bugs... which her immune defense system is entirely unprepared to handle, since it had been completely protected by her "Guardian" power until then. Since her powers return shortly after, they proceed to 'protect' her from syringes and inoculations that could've saved her. Less than a day later, she's dead. She got better.
In Preacher, Friendly Neighborhood Vampire Cassidy makes an It Tastes Like Feet remark about how gravy made from bacon grease tastes like semen (or so he'd assume). Then we find out that in the past, he'd resorted to prostituting himself and giving blowjobs to satisfy his addiction to heroin. Seems slightly less funny, except for those of us with sadistic senses of humor.
Issue #50 of the Marvel G.I. Joe comic (which came out in 1985) included the first issue of the spin-off title G.I. Joe: Special Missions. This first issue revolved around the hijacking of a jetliner by a radical Trotskyist group. Not a far-fetched premise, given the frequency of airline hijackings in the mid-1980s. They even go through the motions of claiming they'll release hostages if demands are met. Then you find out the terrorists' real plan: to use the airliner in a kamikaze attack on the Kremlin to avenge the assassination of Trotsky by Stalin...
There was a story from Paul Dini's run on Batman in which The Joker impersonated a stage magician with a vast teen following. The press revealed that the real magician was dead. The Joker uses a viral marketing campaign to tell his audience that they'll have one last show where they can see that he's not dead. Guess which actor passed away after this comic and printed and what his lasttwo films are...
Also, in an act of insanity, a crazy man goes into a porn theater and shoots the place up. Guess what happened during a showing of The Dark Knight Rises.
There was a 1997 Wonder Woman comic whose cover showed a newspaper with prominent headlines saying that Wonder Woman (aka Princess Diana) had died. A couple days later, the real Princess Diana died.
Deadpool has expressed a love for both the incarnation of Death and Bea Arthur. Now it's a little easier to decide.
Much of what Marvel Comics printed before 9/11/2001, because so many of their stories are based in New York City. For example, early issues of the first iteration of X-Force has the Juggernaut deciding to knock over one of the (pre-evacuated) World Trade Center towers. It made little sense, but over it went. And earlier than X-Force, an ad for Damage Control: The Series had one of the towers about thirty feet off-kilter, but it was 'good enough'. In short, so many otherwise fine stories take place in, on, or around the towers.
During the Zero Hour event, the Post-Crisis Superboy (Kon-El) met the pocket-dimension Superboy (the one keeping Legion of Superheroes from imploding under its own continuity) in Smallville, and Clark-as-Superboy started attacking Kon, declaring himself the real Superboy, to which Kon replied that Clark would have to "Wait 'til I'm dead!" Amusing at the time; less so after Infinite Crisis.
Superboy Prime: Seemed like just a mean-spirited parody of fanboy culture, and then Man of Steel came out, and he went from "parody" to "a little on the nose".
Excalibur, issue 20: a giant interdimensional being ports in with a flash of light outside a town. Rachel and Kitty see the light and assume that the local nuclear power plant had a meltdown, resulting in this conversation:
Linkara (With a disgusted look on his face): The people who have read Ultimatum have this same expression. And you will too when we finally get to it.
There's an early X-Men comic in which a stealth jet is going to be flown into the Twin Towers of the World Trade Center. Fortunately, Wolverine gets on top of the plane, carves his way in, and pulls it up at the very last second. Reading this post 9/11 made it less of a fun action scene and more a harsh reminder that we don't have super-heroes in the real world.
An early cover of Archie Comics' Sonic the Hedgehog called it darker and grittier and made Sonic covered in soot. It really became darker and gritter later on. Much darker.
The character Hazmat in Avengers Academy is an ethnically-Japanese girl with radioactivity based powers who has been described as a "walking Chernobyl". Less than a year after she was introduced, the Sendai earthquake happened, which caused radioactive material to escape from the Fukushima nuclear powerplant.
In Wonder Woman (vol. 3) #14, a character echoes most of the fandom's sentiments by saying "The last thing we want is Amazons Attack: The Sequel". Solicitations for DC's Flashpoint crossover seemed to indicate that it would be Amazons Attack: The Sequel. Luckily Flashpoint was better received and better written and gave an actual reason for their actions that made sense.
In an 80s issue of New Warriors, Speedball and Night Thrasher have this conversation about Speedball's powers. This side of Civil War and "Bleedball", it's not so funny:
Night Thrasher: Robbie, the purpose of this session is to find ways of effectively using your Speedball powers in combat.
Speedball: Well, Dwayne... how 'bout attaching humongous spikes to my spandex? That way I could totally impale all the bad guys!
Night Thrasher: Spikes, huh? [Walks away, looking contemplative]
Speedball: Uh, that's a joke, Thrash...
As a tie-in to Spider-Man 2, in the Ultimate Universe Peter saves a stunt double for the Movie!Spider-Man from Doctor Octopus. When the stunt double took off his mask and revealed he was black Peter worried he got Revamped for a moment.
In one Batman comic, Scarecrow sprays Batman with fear-removing gas and kidnaps Robin. At the end of the comic, Batman reveals that he managed to combat his fearlessness-induced recklessness by thinking of a new fear to motivate him - and it's further revealed to the audience that his fear was that the Scarecrow would kill Robin. The Robin at the time? Jason Todd.
In an issue of Uncanny Avengers, Wolverine goes to Toyko to offer the Japanese hero Sunfire membership in The Avengers. When Sunfire asks why he was considered, Wolverine responds by calling him a "walking atomic bomb." Quite a few people online pointed out that the line is either incredibly dickish or very insensitive depending on whether or not the writer was aware of Hiroshima and Nagasaki.
Especially when you consider that in his first appearance, it's established that Sunfire's mom was an innocent child who eventually died of radiation poisoning she received at Hiroshima. This has been Retconned of course due to Comicbook Time.
Kyle: I just want you to be extra careful. That's all I'm saying. Alex was murdered and so was Donna and I think you—
Jade: Kyle— Kyle. I'll be fine. I promise.
Another X-Men example: In the 1990s, longtime couple Cyclops and Jean Grey finally tied the knot. Marvel released a one-shot special, The Wedding Album and included random autolog messages from the reception. One message comes from Shatterstar, who predicts the marriage won't last. Fast-forward about a decade, and Marvel dropping a bridge on Jean in favor of Cyclops leaving his wife for a rival out of left field, Emma Frost.
Shatterstar: Personally, I cannot think of anything less appealing than committing the rest of your air time to a single individual. I give the marriage three seasons, max. Look for early strong ratings, but an early cancellation. I do, of course, wish you two the best of luck, however. May you have many spinoffs.
In the editorial for a 2005 issue of the 2000AD stablemate Judge Dredd Megazine detailed the difficulty the editor (then Alan Barnes) had on deciding whether or not to run a reprint of a 1970s strip Charley's War, a strip about the First World War. The first page of the re-run started with a full page spread of a Zeppelin Raid on London, with frightened citizens running into a Tube Station yelling "It'll be safe down there." To make matters worse the Editor recounted how this dilemma arose on the last day before the deadline, the 8th of July 2005. Ouch. He did, however, decide to run the strip.
There's a small example in a late-80s issue of The Flash in which Captain Cold has finished his term in the Suicide Squad and the Rogues are attending a party in his honor. Cold brings along a cheery letter from Dr. Light which he reads aloud to laughter and comments like "Arthur's always a card!" Wally and his girlfriend "crash" the party later, and they end up getting along pretty well despite the initial resentment of him for replacing Barry Allen. Some fifteen years later it turns out that these Friendly Enemies were "chums" with a rapist.
In a flashback issue of Martian Manhunter, Maxwell Lord is one of the members of Justice League International briefly possessed by the manifestation of J'onn's Choco addiction:
I want... I want everyone to just do as I say... all the time! I want Superman to do my errands and Batman to respect me and Wonder Woman to... I want Wonder Woman to... oh, how I want Wonder Woman to!
In The Infinity Gauntlet, Thanos using the titular gauntlet causes all sorts of earthquakes to happen all over Earth. One of those buries Japan in the ocean. Makes one cringe after a similar disaster happened to Japan in 2011.
Back in the early 1990's, Valiant Comics released Nintendo Comics System. One of those comics was Game Boy, using characters from Super Mario Land. The first story had Tatanga and his army invade the World Trade Center. The second story had Tatanga and his army hijack an airplane, then hijack the space shuttle Colombia.
In the Wolverine miniseries from Claremont and Miller, very early on, Wolverine catches JAL flight 007 going from New York to Anchorage to Tokyo. Almost exactly one year later, KAL flight 007, going from New York, to Anchorage to Seoul (in other words, the exact same route except for destination) was shot down in Real Life by Soviet fighters who believed that KAL 007 had strayed over the Kamchatka Peninsula, then a restricted area of the USSR.
In the 1960's story "The Sweetheart Superman Forgot", Superman is exposed to red kryptonite that causes him to lose his powers and his memory. He eventually enters a rodeo, where he's thrown from a horse and injured so that he's paralyzed from the waist down. That story became rather more significant when Christopher Reeve, known for playing Superman, was paralyzed from the neck down by being thrown from a horse.
Intentionally invoked in Atomic Robo: in flashbacks, Robo and his company Tesladyne are based in New York City, and have all kinds of adventures there over the years with super-science mishaps, enemies with old grudges, and general weirdness. Tesladyne moves out of NYC almost immediately after 9/11 because Robo realizes that nobody in-universe would find that stuff surrounding his company remotely tolerable anymore.
Tank Girl had an early story in which the Devil appears on Jimmy Savile's distinctive Jim'll Fix It armchair, and then gets defeated by being made to believe that he is Jimmy Savile. Funny at the time, but now...
Fluttershy is worried about anyone finding about her secret chamber in her micro-issue. Normally, this would be a funny joke, but considering the fan-made animation, SHED.MOV, this can border on creepy.
In Johnny the Homicidal Maniac, there are several insert strips of a character called Happy Noodle Boy, drawn by Johnny himself, who frequently shouts out nonsense phrases at others before being shot brutally by a bystander. Cue the panel later on when Johnny remarks that he was bullied as a kid, and that they made fun of his skinny frame by calling him "Noodle Boy". And then the realization comes that Happy Noodle Boy most likely represents Johnny's desire to give in to his inner insanity before dying and relieving himself of the pain he feels.
One Pearls Before Swine strip featured one of the crocs being disappointed that Steve Irwin's head has never been bitten off. This was published mere months before Irwin's death from a stingray attack.
There was an entire series of strips about Rat running for city council against a dead guy that got spiked because they were due to be published right when Senator Paul Wellstone died in a plane crash (even though they were written more than a year in advance).
Similar to the Desmond Llewellyn incident, Charles Schulz's last Peanuts strip - which consisted of his announcement of his retirement and an amiable, grateful farewell to his fans - was written four weeks in advance (like most comic strips)... and was printed one day after he died.
One late 90s FoxTrot strip has Roger and Andy sitting on the couch. When Andy asks what they're listening to, Roger informs her that some guy went into the wild and recorded the ambient sounds of different environments. "So far, it's pretty relaxing." The third panel has them both looking up as the 'guy' says "Hey, get away from that equipmen-" followed by growls, ripping noises, and screaming. The final panel of the strip has Andy reading the title of the CD over the sound of a burp and birdsong; "In the Midst of Grizzlies". Guess what documentary filmmaker Timothy Treadwell, immortalized in the film Grizzly Man, was doing with his girlfriend when he died. Go on, guess. What's more, his camera captured an audio recoding of his death, but it has never been made public.
In another strip, Roger has a nightmare about being forced to give stock certificates that he had in place for retirement to a Salvation Army bin, to which it is heavily implied that they are even more worthless than nickels and dimes. Concerning what ultimately is happening now, that dream is so real.
Notably prevented: The strip published July 22, 2012 was supposed to be showing Paige in the crosshairs of Jason's squirt gun. However, two days before it was supposed to run, a person named James Holmes wearing a gas mask entered a Colorado movie theater that was showing The Dark Knight Rises and proceeded to wildly fire his gun at the audience, killing 12 people and injuring 59 others. Bill Amend then pulled the strip and replaced it with a repeat of a 2009 strip.
Speaking of those pirates... it should be noted first of all that due to newspaper comics being written weeks in advance of publication, sometimes they'll wind up pulling a Funny Aneurysm after the event in question. Such as April 13, 2008's◊ Bizarro panel.
In a series of Doonesbury strips from the early 70s, Duke Harris, who's based on Hunter S. Thompson, accidentally shoots his assistant. Nearly thirty years later, Thompson accidentally shot his assistant.
Another Doonesbury example... during the early stages of the Tiananmen Square protests, Trudeau ran some strips in which the character "Honey" Huan returns to China for a class reunion, only to be caught up, befuddled, in the midst of the protests. This story arc was dropped once the protests were quelled with a tragic massacre.
Bloom County featured several comics making jokes about the marriage of Princess Diana and Prince Charles (specifically, an arc depicting them spending their honeymoon in New York). This isn't quite as funny after you consider their divorce and her death...
Several Italian Disney comics featured Uncle Scrooge as the owner of a newspaper that always seemed to be teetering on the edge of bankruptcy. This was always played for laughs. It doesn't become so funny once you consider the present situation of print media. It gets even worse by the fact that some writers portray the paper as a normal functioning respected news source, giving a reader that reads the stories in a certain order the idea that the paper was a successful venture that started spiraling into the abyss.
While we're on Scrooge: a Don Rosastory has a floating money bin (It's a Long Story, involving alien phlebotinum) flying through twin towers◊... as you can see in the image (one of the balloons has an asterisk), a recent reprint has a footnote saying the comic was made before 9/11 (1997, to be precise).
A literal example occurred in The Far Side: a strip involving Dick Clark aging 200 years in 30 seconds on national TV. That's a pretty accurate description of what has happened to him since his stroke back in 2004. And now that he's dead at 82, it's even worse.
Take a look at this political cartoon from 1870, using anthromorphisised countries to depict the situation of Europe before World War One. Now, notice how Germany's hand is resting on Belgium...
In an early Zits strip Jeremy bemoans the that his generation doesn't have an epic, "where were you?" moment like the Kennedy assassination. Then came September 11th...
A 1934 Mickey Mouse comic had Mickey and Minnie kidnapped by smuggler Bad Pete. One strip here◊ depicts opium being smuggled...disguised as "bath salts".
Was narrowly averted by the satirical Swedish comic Arne Anka. The artist had just finished a strip that ended with Arne and his friend Krille going on a shooting spree against snooty waiters at Discoteque "Sturecompagniet" in Stockholm, when news broke on the radio that there had been a Real Life shooting at "Sturecompagniet". He quickly scrapped the strip and drew one where Arne and Krille discuss violence in society in general.
And that strip ends with an over-the-top moment where a reporter blows up an amusement park and faxes a report about the dead children at the same time. Grotesquely over-the-top at the time (1994), but then in 2012 came the Utřya-massacre ...
A Calvin and Hobbes strip has Calvin criticize Susie's drawing of a home with a flower garden, instead claiming his manlier drawing of B-1 planes nuking New York. The September 11, 2001 attacks put the strip in a Dude, Not Funny! stance.
In De Ark van Nero (1952) Nero builds an arc because of a great flood that will put the entire world under water. It later turns out to be All Just a Dream, but only a few months after the story was finished Belgium and the Netherlands were in 1953 indeed hit by a disastrous flood, killing many people in the Netherlands alone.
In Het Ei van October (1955) Nero's plane crashes into a New York skyscraper, difficult not to think about the 9/11 terrorist attacks since 2001.
In De Grote Geheimzinnigaard (1993) Nero wishes Colombian drug baron Pablo Escobar to the Moon. Later that exact same year Escobar was shot by the police.