Doctor Strange: Doctor Strange, in a moment of grief after losing Clea, wished he were dead. Enter D'Spayre, who put him through a series of Mind Screws so painful that Strange nearly took his own life.
Black Panther: In Black Panther (2016), the two new antagonists, Zenzi and her ally Tetu have been trying to overthrow T'Challa, but in order to put a more democratic government and just society. However, their benefactor (financially and technologically), the Iron Monger, warns Tenzu about one of the core tenants of revolution:
Figment (Disney Kingdoms): After Blair and Figment disappear through a portal from the mesmonic converter into a realm of imagination, Chairman Illocrant attempts to shut down the machine by calling for order. Unfortunately, this summons a robotic being called the Singular and his robot army from a place called Clockwork Control and their idea of order is not what the chairman had in mind.
The Planet Hulk storyline. After a fight between the Hulk and the Thing leaves Las Vegas in ruins and a dozen people dead, the Illuminati - specifically Tony Stark, Reed Richards, Doctor Strange, and Black Bolt (Professor X wasn't present and Namor voted no) - decided that Hulk was too dangerous to be allowed on Earth, so they came up with a plan to send him to a peaceful world with no intelligent life. The green behemoth always wanted to be left alone, why not grant his wish? Of course, everything goes horribly wrong.
The 2011 "Heart of the Monster" arc in The Incredible Hulks is built around this trope - Hulk and his team encounter a Wishing Well. Everyone involved knows what it will twist every wish it grants. What they don't know is the intentions of the Red She-Hulk, who used it to wish doom on her ex-husband.... if she meant it, his circumstances are going to improve, but if she liked him... As it turns out, she hated him at the time, meaning all of his dreams briefly came true.
The beginning of Immortal Hulk introduces Jackie McGee, a young reporter who wants to become a Hulk to express her rage at systemic racism. She doesn't quite realize what a horror-show the Hulk has made out of Bruce Banner's life until she meets him in person.
The Alternate Universe story Hulk: The End, shows the Hulk finally getting what he always wished for: to be left alone. Completely alone, not even Banner nagging in the back of his mind. He almost immediately begins to regret it.
Quasar: In the storyline Starblast, the Big Bad Skeletron seeks to obtain the Star Brand. After a titanic battle with the Stranger, he gets his hands on the power, only to find out the Stranger stranded him in the now-lifeless home of the New Universe, the Stranger having pulled its Earth to the 616 universe
Ultimate FF: Subverted. Without more ideas on how to deal with the monsters of the incursion, the team (except Sue) wishes that Reed was there. Then, Coulson sent the cavalry. Sue thought that it was Reed, all the red herrings suggested that it was Reed, but no: it was Victor Van Damme.
The core problem with the Sentinels, whose prime directive is some variant of 'protect humans from mutants'. They keep being rebuilt because some mutant-hating bigot or other doesn't realize that mutants are human, with the X-gene being a genetic quirk comparable to having red hair or being XXY male. This tends to lead to Skynetimpressions.
When a powerful Reality Warper throws a fit, really bad things can happen. Shortly after House of M, the Scarlet Witch's Laser-Guided Amnesia that had suppressed the memories of her children was undone. In a fit of rage and grief, she wished for a world with no mutants. The result? M-Day.
At the beginning of All-New X-Men, the X-Men are disgusted with their ex-teammate's Cyclops militaristic turn, to the point Iceman states he wishes young Scott saw what he's turned into. Beast somehow thinks that jeopardizing the entire time-space continuum is a great idea and brings the original X-Men to the future so they shame adult Scott. What happens instead is the Original Five are originally horrified, but then they discover the modern X-Men twisted and withheld facts to make adult Cyclops look worse. At the end of Battle of the Atom the Original Five decide Wolverine and his X-Men aren't better than adult Cyclops and can't be trusted, and they all join older Cyclops' side.
In Immortal X-Men, Sebastian Shaw makes a deal with Mother Righteous to gain control of Krakoa. He gets it... during Fall of X, when the island is abandoned and lacks all the financial and political clout Shaw was actually interested in. Righteous lampshades it:
Mother Righteous: You made a deal with a magician. A speller. A storyteller. You make a deal in a story, and it’s never quite what you wanted.
In Doctor Strange (2016), Kaecilius is working to bring Dormammu to Earth as he believes that humans will achieve eternal life in Dormammu's Dark Dimension. In the conclusion, Strange forces Dormammu to leave Earth and bring his followers with him. Too late, Kaecilius realizes that Dormammu's offer of "eternal life" meant being transformed into a horrific mindless creature in everlasting agony inside Dormammu's home. Strange even lampshades it by stating, "Well, it's everything you've ever wanted - eternal life as part of the One. You're not gonna like it."
Doctor Strange in the Multiverse of Madness: Scarlet Witch desires to be a mother by taking her children from another universe. She gets exactly what she wants thanks to America Chavez sending her there... but the kids are left understandably horrified at the monstrosity she's become.
Live-Action TV
Agents of S.H.I.E.L.D.: In Season 4, Dr. Radcliffe and Aida created an entire virtual world called the Framework to keep agents docile while they are replaced by Life Model Decoys. Aida was instructed to fix the single greatest regret of every new entry, and had to reboot the simulation several times to reconcile them all together. The problem is, her "fixes" only addressed the basic problem with no consideration for context, so the agents aren't 'themselves with less angst', but very different people living in a world where HYDRA won, and their emblem is emblazoned on the side of S.H.I.E.L.D.'s headquarters. Later episodes detail the specific changes:
May killed a little girl because she was a crazy Inhuman with brainwashing powers who gets high off the suffering of other people. May wished that she didn't have to kill the child. In Framework, May spared her. Except the girl was still a crazy Inhuman with brainwashing powers, and went on to cause a very public incident at the Cambridge, Massachusetts school she was placed in after being brought to America. HYDRA happily capitalized on this incident to get themselves in power by stoking anti-Inhuman sentiment sky-high and presenting themselves as the only solution to the Inhuman menace. May now regrets not killing the girl far more than she ever regretted killing her, and blames herself for allowing the Cambridge Incident to occur. She now loyally serves HYDRA as an Inhuman hunter.
Coulson always wondered what his life would have been like if he hadn't joined S.H.I.E.L.D. In the Framework, he turned down Nick Fury's offer and became a high school history teacher instead. He's also a coward who repeats HYDRA's lies whole-heartedly despite not believing any of them for a second, even allowing them to take "subversive" students directly out of his class. It's implied that his absence is what allowed HYDRA to rise in this reality, as he was always a stabilizing influence on S.H.I.E.L.D. in general and May specifically.
Fitz's father walked out on him as a child. In the Framework, he never left. Except he's still a giant asshole who thinks Virtue Is Weakness and outwardly showing emotion of any kind is for pussies. He beat all empathy out of his son, resulting in Fitz becoming a Mad ScientistTorture Technician who would make Mengele blanch.
Mack's daughter, Hope, died as a baby, resulting in him splitting with his wife. In the Framework, she lived. That worked out mostly okay for Mack, though his wife is missing and he never got around to joining S.H.I.E.L.D. He mostly keeps his head down around HYDRA, but when they push too hard he joins with S.H.I.E.L.D. because he is worried he is setting a bad example for his daughter. .
Mace is a Fake Ultimate Hero who just wanted to do some real good. In the Framework, he is a real Inhuman instead of just using a Super Serum, and he leads the remnants of S.H.I.E.L.D. as "the Patriot". He ultimately dies saving a kid from a collapsing building, mirroring the event in the real world where someone mistakenly believed he had saved someone from a collapsing roof and it got blown out of proportion. This also kills him in the real world since Your Mind Makes It Real. Like Mack, Mace probably considers this a good deal in the end.
Video Games
Iron Man 3: The Official Game: The Living Laser was just a nobody who wanted power, and was turned into a cybernetic being by A.I.M. to help accomplish their goals. While initially pleased with his new powers, he eventually regretted how he was no longer human and continued to work for A.I.M. in the hopes they would turn him back to normal.
Western Animation
The Spectacular Spider-Man: In "Group Therapy", Peter has to deal with Doc Ock forming his Sinister Six and ends up outclassed. After a rough day, he goes to sleep, saying "I wish I could just wake up tomorrow, with Doc and his merry morons back in jail." The Symbiote, whom he was with at the time, grants said wish... by puppeting Peter's sleeping body to fight against the Six (which it does manage to win), which leaves Peter both exhausted and more susceptible to the manipulations of the symbiote (which include being too ill-tempered to talk to JJJ, who called to inform him that his aunt has been hospitalized from a heart attack.)
Ultimate Spider-Man (2012): The main arc of season one is that Norman Osborn wants to either have Spider-Man's powers, or control a being with those powers (which is why he had Dr. Octopus create Venom). In the season's Wham Episode, Dr. Octopus turns on Norman and injects him with the serum that turns him into the Green Goblin. He has the powers he always wanted, but at the cost of his sanity and humanity.
