In Deviants of Art the event that kicks off the plot is the depressed and frustrated hero of the story makes an exasperated wish absentmindedly. Played with in that the wish is not immediately granted, instead it's only after the main character's situation gets better and something happens in the Internet that his wish is granted. While he does like what has happened in terms of going to another world, he instantly thinks of his family and asks how he can go home.
A character playing a D&D game gets a ring of three wishes, much to the chagrin of the DM. The character immediately wishes for more gold than he knows what to do with, and his player is instantly crushed by a giant gold boulder. When the previous wish is reversed while still losing the wish, he then wishes for a million gold pieces, and receives gold pieces so small that he "might be able to afford an ale with them". When he finally gets a wish written up by a lawyer in order to avoid any exploitable loopholes, the DM relents and has no choice but to grant the wish. And then the player's character gets eaten by a dragon.
Another DM had a player who wished for an infinite gold mine. His wish was granted, and the player's character was instantly teleported into a mine of solid gold, stretching forever in all directions...
Death of Insanely Overpowered Fireballs from Irregular Webcomic! wished to get his job back after getting demoted. He got his job back, to process all the people who have died when the Irregular Universe was torn apart from Time Paradox.
Parson: "I mean, then... what's the lesson supposed to be here, Wanda? 'Be careful what you wish for?' This isn't what I wished for!"
Wanda: "Hah! You didn't wish for this world, Parson Gotti. It wished for you.
Also, the "Ultimate Warlord" spell. Why did Stanley get Parson? Well, this is how he described what he wanted:
"I want him to be obsessed with war! Somebody who plans wars and kills his enemies for fun!note Parson enjoys playing table top wargames, a lot I want somebody who snacks on Gwiffonsnote Gwiffons look exactly like marshmallow Peeps. and eats Marbits for breakfast!note Parson calls marshmallow bits (like the kind you find in Lucky Charms) "Marbits= Marshmallow bits".
When Don King asks Jillian what sort of heir she wants, she says she will be happy with anyone so long as they have the Flight special. Don King muses that she wants yet another sword, and warns her to be careful of the trope. Boy does Fate ever deliver. Not only does her son pop with two powerful specials, including Flight, he also pops with an attitude even worse than her own, making him a nightmare to manage.
Roadkill: Wish One: I want all my wishes loopholed out of any negative or ironic consequences. Wish Two: Apply wish number one to itself ex post facto. Wish Three: Make me the effin' master of the Universe NOW.
Any plot in The Wotch involving Djinn will feature at least one of these types of wishes. It is explained that some Djinn do it out of spite for the human race, others do it because they've been summoned through a cursed bottle that mandates their wishes backfire (with a "generous" interpretation of what constitutes a wish, to boot).
He still gets bitten a little. He wished that everything the enemy had stolen be returned to Fenwick. Not just things that had been stolen from Fenwick. And the enemy had a very long career of stealing things. There are now entire store-rooms of 'returned' loot, much of which is unidentifiable and now worthless.
Also played straight with Rahan, when he wishes he could see Quentyn's face after a prank involving pillows and tar goes off. He does—after Squidge sends the prank completely sideways.
Very old Vera Salt of Magellan found a genie and wished herself to be younger. She started to age backwards until she was a child. Then, she wished for a way to age herself and had to siphon age from others over several centuries in order to maintain a stable age. Finally, when she was in custody, she used her last wish to wish herself free and ended up dying of old age.
In Homestuck, the pre-Scratch troll players are hinted (and stated outright in one case) to have gotten exactly what they wanted for their lives in the retconned universe they created... at a tremendous cost.
Aranea wished she could be outgoing and adventurous without caring about what other people think of her. Then she helped perform the Scratch and got her wish, at least vicariously... but at the cost of her people being enslaved by a devil-figure and being driven to near-extinction; because she didn't really care about other people, she did nothing to prevent any of the suffering.
Kankri wanted to fight for social justice, and his Scratched counterpart was a Messianic Archetype... who ended up with an even more painful end than Jesus, for significantly less accomplishment.
Damara wanted to serve Lord English, and her counterpart suffered so much in doing so that she was Driven to Suicide... and death was denied to her for centuries until she provided Lord English with a new slave.
Meenah wanted to be a horrific absolute monarch without personal responsibility regarding her society's rigid White Man's Burden (which fell on her the heaviest), and her counterpart was just such a tyrant... who was secretly forced to obey the Bigger Bad and who was so cruel a tyrant that she tortured the counterpart of one of Meenah's friends, who Meenah never wanted to harm.
Same for Kurloz, who became head of his church and likewise killed those his counterpart cared about
Porrim wanted to take care of Kankri; she did so, then watched him killed and was made a slave
Meulin wanted true love, got it, and then saw it killed in front of her
Latula wanted to bring justice and protect the innocent, and was lynched for it
Cronus wanted to be part of an interesting story and have a dramatic rival; his rival took actions which ended with him being murdered by a clown. He'd also stated that he wanted to be treated as he deserved; he was treated exactly that way.
Mituna wanted to help his friends and was made into a living battery/engine part by one of them
Rufioh wanted to be a hero, and led a great rebellion... which failed and made things worse
In Doc Rat, Wilbur Fuzz is shaken when after all his jokes about heart attacks, he actually has one. He thinks of Crying Wolf. The paramedics — wolves — tell him that they came, and he should be careful what he wishes for.
In Ménage à 3, central character Gary implicitly wishes, in the second panel of the very first strip, for a more interesting life. He gets ... to be the central character of this comic. Actually, it's not entirely a bad life, but he gets things like lots of women wanting him without ever getting a clue how to handle the consequences. Other characters in the same comic also tend to get things that they think they want, while lacking the emotional maturity to deal with them.
In The Order of the Stick Nale demands independence from his father, saying that he wants NOTHING from him, and specifically including nepotism, charity, and pity. Nale tried to overthrow his father, constantly insults him and tries to undermine his authority, and killed his best friend and valuable ally Malack. So when Tarquin stops treating him like his son, and treats him like he would anyone else who's done those things, he immediately kills him. He points out as Nale dies that he'd have been dead years ago if Tarquin hadn't been protecting him.
Lei'ella warns Acheron of this in Inverloch when he says he wants to find out what happened to his Disappeared Dad. She's right. Finding out that Roche was murdered by an elf gives Acheron a Heroic B.S.O.D. and nearly makes him abandon his quest.
Fox of Curtailed will take a request perfectly literally, but only if doing so would be funnier than just saying no.
Kill Six Billion Demons: Our heroine Allison gets thrust into action, adventure, and really wild things. In this strip, she expresses her dissatisfaction to the goddess Mottom, absolute ruler of one-seventh of all creation:
Allison: I've been trying my whole boring mundane fucking life to escape being a nobody, but you know what? Now I want it back.
Mottom replies that once Destiny has sunk its claws into you, there's no way back.
The Norway segment of the prologue happens in a village to which the only land road has been destroyed by a storm, making in rely on boat traffic for its supplies. One of the named characters thinks the road should never be repaired, that they should rely on boat traffic permanently and that it would be fun if the electricity went out for a few weeks, so they could live like in old times. When Norway is seen again After the End, it seems to have returned to a viking-like lifestyle.
Reynir ending up as a stowaway to the crew can be summed up by this piece of imaginary dialogue:
Reynir: I'd really like to visit Denmark. Gods: Whoops, sorry kid, we forgot the country's mainland is now a Forbidden Zone. You actually meant that one island that's still inhabitable, didn't you?