In an issue of Uncanny X-Men from 1984, we get a flashback (-forward?) to Rachel Summers' Crapsack World of her Days of Future Past, where it's revealed that among the other actions to happen in the war against the mutants, someone destroyed the World Trade Center with a bomb (one panel shows the Twin Towers in ruins). Unthinkable in 1986, but cringe-inducing after 1993 and absolutely eerie after 2001. Bear in mind that, if not for Comic-Book Time, 2001 would likely be the actual year that the World Trade Center was destroyed in Rachel's timeline.
Similarly, one issue of Wolverine's own comic book featured an enemy flying a plane into him. While he was standing on top of the World Trade Center.
After Ozymandias detonates his psychic squid in Watchmen, an airship can be seen crashed into the side of a New York skyscraper.
G.I. Joe: In an issue of the Marvelseries the Joes go against a Middle-Eastern dictator that commanded an army of radical zealots and was backed by a Terror group. Twenty years later America went to war against several Middle-East countries ruled by dictators backed by zealots with ties to terrorist groups.
On the subject of 9/11, the TransformersMarvel Comics featured Galvatron visiting an alternate universe, where New York had been devastated and Rodimus Prime's corpse was strung up between the smoking stumps of the Twin Towers.
More fun with 9/11 in the 1995 Marvel Comics tie-in novel Spider-Man: The Octopus Agenda by Diane Duane: the book's climax features Spidey's attempts to foil the plans of Doctor Octopus, who's planted a bomb in the World Trade Center.
There was also the Spider-Man/X-Force crossover where the Juggernaut destroyed one of the twin towers in the course of his brawl with the heroes.
9/11 times four, and this time not from Marvel: An issue of Superman sent DC into a panic, when the LexCorp Towers (Metropolis' version of the Twin Towers) were shown to be in a state of near total collapse after being hit by an alien spaceship. The day that comic was due to hit newstands? September 12, 2001. DC assured retailers that they would be allowed a no-fault return for the issue, given the situation, and encouraged them to make use of it. Few, apparently, did.
It's worse than that the issue, taking place after a global invasion, had several pictures of buildings in ruins... Near the picture of the LexCorp building was one of the ACTUAL twin towers, with blast holes at roughly the SAME place as where the planes had hit in real life!
But topping them all would have to be The Dark Knight Returns by Frank Miller. Published in 1986, the story involves Two-Face plotting to blow up "The Twin Towers" in Gotham. Luckily, he's stopped by Batman. Shortly thereafter, an electromagnetic pulse caused by the detonation of a powerful nuclear warhead in the western hemisphere knocks out all power to seemingly the entirety of America. A 747 then falls out of the sky and crashes into the Twin Towers, blowing them up and setting all of Gotham on fire.
A 1995 Judge Dredd arc had Dredd travel back in time to prevent an alien disease from spreading. To do this, he had to blow up a plane...over New York...in 2001. The twin towers are visible in the background as the plane crashes into the river. The scene was even on the front cover with the caption "Airport 2001".
In a one-off story from 1978, a criminal demonstrates his power by causing the World Trade Center to collapse. Ouch.
V for Vendetta features a pedophile priest. Already creepy at the time, it takes on a whole new layer of uncomfortableness with the Catholic child molestation scandals that have broken out since. There have been accusations for centuries, which probably inspired the character, but they really hit broad public awareness in The Nineties.
The scenes in Uncanny X-Men #101 where the space shuttle breaks up on re-entry and crashes in New York and the similar sequence from the 1990s' Spider-Man: The Animated Series were intended to be merely dramatic when they were created, but some find it difficult to watch them without thinking of the Columbia tragedy. The Spider-Man episode is the most similar to the real disaster, which makes it REALLY creepy.
One Wonder Woman comic had a fake newspaper on its cover with headlines proclaiming Wonder Woman's death and referred to her as Princess Diana. Guess who died a week later.
There's a late 70's issue of Marvel Two-In-One where the World Trade Center catches fire.
The Batman storyline A Lonely Place of Dying has a scene where Two-Face almost decides to blow up the twin towers just to piss the dark knight off. This is made worse by Bruce Wayne simultaneously considering holding a massive charity event there to provoke him into attacking.
Another 9/11 one: The Big Book Of The Seventies (published in 2000) had a section on the rise of terrorism, which ended with the first WTC bombing.
One Nintendo Comics System issue from 1990 had an establishing shot of the Twin Towers with a dark cloud looming above.
One of the very first Teenage Mutant Ninja Turtles Mirage comics had the bad guy threatening to collapse the Twin Towers if he wasn't paid a ransom of thousand of dollars. A new re-print, which had a note at the very edge of the paper "(Remember this comic was released a long time before 9/11)"
An in-universe example for the Marvel Universe. One issue of the late 90s Captain America comic had Cap foiling a plot by a Skrull to impersonate him and cause widespread chaos in the United States. What does he say upon defeating the Skrull?:
Cap: Next time, take over a planet without me on it.
Cue 2008's Secret Invasion, in which the Skrulls do take over the planet without Cap on it, as he had been supposedly dead at the time.
In Ultimate X-Men, mutants are more discriminated than ever before and can be held without a trial even if they didn't do anything wrong, and you can even legally kill them. At the time when it was written, it was meant to show how Ultimate Marvel is different from Earth-616. And then the National Defense Authorization Act came.
The Choose Your Own Adventure Dole-Playing Game You Are Maggie Thatcher was a Character Exaggeration of the much-reviled prime minister, and yet the whole thing did not look all too implausible in real life. For example, one of the options was to privatize the police force, which David Cameron actually proposed years later.
An in-universe one DC one: Issues #20-#21 of the New Teen Titans comic (May-June 1986). The Titans were (temporarily) mostly broken up after incidents involving or happening roughly around the time of Crisis on Infinite Earths. Wonder Girl, who is left in charge with an empty nest, calls in Aqualad, a newly-minted Flash, a Hawk without Dove, Jason-Robin and Speedy. At the request of King Faraday, they help to protect a peace conference which is being threatened by Cheshire. This was where it was discovered Speedy and Cheshire had a child together. Issue #21 closes on some supposed to be heart-warming reconciliations between Terry Long and Wonder Girl and also Speedy and Cheshire, including him getting to hold his daughter for the first time. Also, Wally getting to explain his new role as The Flash to his hero-avoidant then-girlfriend Francis Kane. Now, look at these events through the lens of:
Speedy and Wally West still apparently have strong feelings for Wonder Girl, well after their teen romance fizzled according to later comics. Oh and Lian is killed when Prometheus destroys Star City and chops off Speedy's arm too.
King Faraday being the (possibly mind-controlled) villain, Gamemaster.
Wally-Flash being erased from existence by Barry Allen as a result of Flashpoint, made worse by the fact that when fighting a deranged Reverse Flash (who had a breakdown and literally thought of himself as Barry Allen) cursing Wally and leaving him to die out of anger over how everyone loved Wally more as Flash and was furious at how fast he was forgeotten
Jason Todd being the voice of reason among his older, more experienced peers and then not receiving a statue in the memorial hall upon his death for this and the work to free Raven as if they were embarrassed.
Having Speedy, Wonder Girl and Flash return to Cheshire, Terry Long and Francis Kane with the idea that this is a relief to them. All three of these couples later go nuclear, one of them literally.
Having Hank Hall (Hawk) be a nearly-murderous bastard as a hero, when later he becomes the JSA villain Extant, who slaughtered half of the team.
Batman's origin story will now qualify as such. In most mediums, his parents were shot by Joe Chill outside of a movie theater (or in the case of The Dark Knight Saga, an opera theater). Let's just say there are roughly 7 times as many Martha and Thomas Waynes dead now after the showing of The Dark Knight Rises, when the premiere at Aurora Colorado had a madman shooting and killing as many as 14 people as they were leaving the premiere.
Simliar to the aforementioned scenes in The Dark Knight Returns involving Gotham's Twin Tower, a scene in Returns featured a gunman shooting people at a Batman themed movie theater.
In the only Captain Electron comic, the titular hero is called to rush to Manhattan while in the middle of a separate "computer science" mission. When he arrives in New York, he finds a plane...buried halfway in the Chrysler Building.
The Avengers 111, 1973. Magneto had captured the X-Men and several Avengers, turning them into People Puppets. Only 3 Avengers were still free, Thor, Vision and Black Panther. So sure about his strenght in numbers over the Avengers, and with the Scarlet Witch dancing under his control, he said "But they are decimated, Piper - DECIMATED!"◊ (bolded in the original). He would surely come to regret those words: in House of M the Scarlet Witch, mad and with reality warping powers, turned all mutants except 192 into normal people without powers, including Magneto. The name of the near-extinction of mutants? "Decimation".
There's also the fact he had Wanda dancing for his amusement; given her choice of outfits and the way everyone used to react to her, this was probably for his own tiltilation. Bare in mind, a few years later, Magneto would discover that Wanda is, in fact, his daughter.
The Marvel Civil War was painfully cringe-worthy to begin with. Now, let's just say that it starts with a disturbed individual attacking an elementary school in Connecticut and leave it at that.
In last issue of Brian K. Vaughn run on Runaways entire creative team wonders what will happen with the characters in next ten years. One of the comments mentioned they'll probably be all dead. Near the team's tenth anniversary two of the characters are in book dedicated solely to killing teenage superheroes.
The 1990-91 Foolkiller limited series climaxed during the summer of 1991 around the same time that Jeffrey Dahmer was arrested and his long killing spree revealed. Although readers knew who the Foolkiller was all the time, this is when the general public and his former friends and acquaintances learn of his identity on the news.
Elvis Shrugged: In the story, the record business has collapsed due to so many quality musicians leaving, causing record sales to plummet. This was published in 1993, prior to the debut of the World Wide Web and, later, the rise of Napster and iTunes, which would cause the sales of actual CDs to plummet, not due to a significant change in what was popular, but because it was easier and cheaper.