An Irregular Webcomic! strip involved a character who is obviously not Steve Irwin not dying from a fatal snakebite because Death was on strike. It had the annotation, "Oh come on. You all knew Steve wouldn't die." The strip in question came out on the exact day of Irwin's death (although it was composed some three weeks before). This is pointed out in the annotation.
Five years before that, during a Halloween special, Uozin had been stabbed in the heart by a demon's spear. A demon spear that was referred to as a 'squid-on-a-stick', no less...
Megatokyo has this fairly early strip depicting what would happen if Fred worked without Rodney, or vice-versa. Two years later, Rodney stopped contributing to the comic; the old joke strip turned out to be, in many ways, pretty accurate.
1/0 declared "war" on another webcomic on September 11th of 2000.
An early running gag has Roger vehemently deny being a werecoyote, despite the fact that nobody accused him of being one. By the time he reveals that he is one, the strip's taken a dark enough turn that a terrible bloodlust, to which his mother has already succumbed, is a major plot point.
Another early story has April and Roger get possessed by ghosts inhabiting a television set and a hairdryer, respectively, to do battle. Later stories show that Roger is particularly vulnerable to possession by Satan in his werecoyote form, and April's gradual progression to Yandere and eventually Manipulative Bastard is implied to be at least partially due to Satanic influence.
The king of them all, however, is in the earliest storyline of note: A paranoid Marsha stabs Mike, hospitalizing him. Immediately afterward, she blames April, because "Miss Wimpy didn't want any bloodstains on her wimpy clothes!" It's Only a Flesh Wound, and Mike (a consummate Manipulative Bastard) recovers perfectly, then leverages Marsha's guilt to start off their relationship. In a much later storyline, Mike is Killed Off for Real when April, following an argument with Marsha about her relationship with Mike, fatally stabs him.
The punch line of this strip is a retroactive example. The aneurysm doesn't come until you remember (or read, if you hadn't already) the Start of Darkness prequel in which you realize just how low Xykon can go (and how painfully aware Redcloak is of it).
There's also the Cliffport police chief talking about how the mayor was going to have his head on a pike because of the ruckus Nale caused. A couple of strips later, Nale cuts off the Chief's head and impales it on his sword.Mmm...shishkabobs.
"It may be the last night alive for many of those girls you just told to 'chill out'. It might even be the last night for you, or one of your friends."
Elan picturing Roy as a surrogate older brother becomes less funny when you realize that Roy really did have a younger brother who might have become a bard, had he not died in an accident at a young age.
In one strip, Xykon says this to Redcloak after he murdered Tsukiko.
Xykon: If you had to smoke her, you had to smoke her. Hell knows I've had occasion to off an uppity minion in my day. This sounds like Xykon being his usual Affably Evil self, until you've read Start of Darkness, where Redcloak's younger brother attempted to kill Xykon to avenge his family, and Redcloak was forced to kill him. Its one of many ways Xykon subtly torments Redcloak.
In this strip, Haley claims it'll take "200-foot tall flaming letters" to help convince Elan that his Affably Evil long-lost father is really bad news. This strip makes a rather dark joke about it when that turns out to be the case, as Elan his horrified when his father spells out Elan's name in the burned-alive bodies of rebellious slaves, the same ones Haley and Vaarsuvius freed in an earlier strip.
A rare case of averting this trope: In the print edition of the first run of comics, there's a previously-omitted comic during the battle with Xykon in which Vaarsuvius, paralyzed by a ghasts' touch, sits helplessly while a trio of demon roaches sits on his/her head and crack wise. Why was it omitted from the online comic? Because the morning that it was scheduled to be posted, Christopher Reeve died. The author (wisely) pulled it, only letting it see the light of day as a "bonus strip" over a year later.
ThisDominic Deegan strip features Greg complaining about his magic being called a "super power". A few years later, there would be some agreement on that point.
Back in 1999, Penny Arcade published a strip about Duke Nukem Forever, which became funnier with each year of the game's famously long development (which, back then, had only been over two years.) Almost a decade later, its developer shut down. Especially good because the strip more-or-less illustrated whyDuke Nukem Forever didn't come out when it was supposed to, long before anyone outside the production company knew. The company just kept playing around instead of delivering the promised game to a distributor (the distributor changed midway); by the time they took the deadline seriously (Take-Two was less patient than the previous distributor), they were no longer able to get the money to complete it. Of course, now that the game is actually coming out (and debuted at PAX no less!), the strip has changed to a Hilarious in Hindsight.
Kat's belongings sometimes have the names of bands printed on them. In this page, her shirt reads Sparklehorse. Mark Linkous, who led that band, committed suicide 2 months prior to the page being published. Considering the 30-page buffer kept by the author, it would seem that the page itself was made a few weeks before it happened. It has been confirmed by Word of God that this was intended as a tribute.
After triggering a warning klaxon, Annie quite calmly states that she dislikes alarms. A few chapters later, there's a flashback to when she was much younger and had to experience a ghost child's memories of dying in a house fire, complete with smoke alarms.
This strip of A Softer World illustrates what seems like a rather improbable idea of what causes terrorists to be terrorists. But a later sociological study discovered that many of them don't really care about their cause, and if their mission is actually accomplished they just move on to another extremist group. It concluded that a large proportion really aresocial rejects who can't find friends anywhere else, and are willing to kill for the sake of that bond.
In YU+ME: dream , in Part One, Jake sarcastically tells Lia, Im just pretending to be gay for all of the social benefits it brings, the joke being that so far in the comic, hes caught nothing but flak for his homosexuality. In Part Two, after weve found out that that everything in Part One was essentially a reality show, its revealed that the actor who played Jake is actually a straight douche who won an Emmy Award for his portrayal of Jake. The commentary on this page suggests that he primarily won the award because of the (mis)perception that its a huge challenge for a straight actor to play a gay character.
A EGS:NP strip has Susan and Sarah discussing vampire romance novels and how they would translate into real life. It turns out she was almost killed by the way she described would happen in a vampire romance.
Abraham being incredulous about the nature of Ellen's "curse" is funny until you realize that he's angry/freaked out because he vowed to kill whatever the diamond made, and that means he would have to kill something human.
Roommates has/had a Running Gag about Jareth failing to do good despite his best intentions and efforts... after the Dark!Jareth arc that got some pretty heavy subtext. As a fictional character he can't defy the story and his role in it, doesn't matter how desperately he may try.
In Drowtales, thisfiller of Snadhya'rune demanding a refund for Kalki was put up during the publishing of chapter 46, and became a lot less funny at the end of that chapter when Snadhya brutally murdered Kalki and declared her nothing but a tool.
In an Exterminatus Now strip, Lothar theorizes that Australian entertainer Rolf Harris is actually a pedophile based on his mannerisms and elements of his show. Eastwood reacts furiously and storms off in disgust, calling Harris a "national treasure", with the joke being that only someone as cynical and selfish as Lothar could ever think such a thing. Come 2014 and Harris is arrested for child molestation, meaning Lothar was right all along. To make matters worse, the strip was accompanied by a disclaimer reminding the readers that the opinions of the characters didn't necessarily coincide with the opinions of the authors (despite said characters being self-inserts). Which means presumably they all thought the world of Harris as well until the news came out.
ThisBrawl in the Family comic, doubly so, because not only did the Ice Climbers end up getting cut from Smash for Wii U/3DS, Snake, the other character in this comic, did as well. To make matters worse, the author comments below the comic mentions the possibility of the 3DS not being able to handle the Ice Climbers, which ended up being the reason they got cut: the 3DS just doesn't have the power to keep up with four sets of Ice Climbers at once without serious lag or framerate drops.
In this comic, Nintendo mentions how she's told investors a million times that she's NOT interested in making iOS games and asks them to stop asking her about it. Some weeks later...
One of Nintendo's terrible advice "spam mails" says to "replace [her] boss", referring of course to Nintendo's CEO and president at the time, Satoru Iwata, who was often critizised by analysts and investors. After Iwata's death in 2015, suddenly this became a lot less funny...
This comic of Bug Martini talked about attacking Paris; it became a lot less funny in 2015 after the Chariie Hebdo shootings that January and even less funny after the much deadlier attacks ten months later.
ThisFull Frontal Nerdity with Death apologizing for a rash of celebrity deaths in early 2016 ends with a joke about how Abe Vigoda was safe. In real life, Abe Vigoda died (of old age) less than a week after the comic was published.
In Awful Hospital, the resident Mad Doctors and their Comically Inept Healing attempts get a lot grimmer in retrospect when the protagonist learns that the Hospital and, by association, the very concept of medical care is being sabotaged, driving the doctors insane and eroding their ability to understand what's helping or hurting their patients.
Dr. Phage:Gaps in my understanding of reality are widening. I can feel it. ... There is little we can do but to continue our work as healers to the best of that ability, however fractured that ability might become. Dr. Phage: We'll have those hearts pumping healthy yellow bile again in no time!