Marvel's Absolute Carnage event kicks off with the death of Lee Price aka Maniac, a Jerkass former host of the Venom symbiote and the then-current host of the Mania symbiote notorious for his irredeemable personality and actions towards others, traits that made his killing off via Carnage very satisfying.
Marcus, from The Avengers #200 who used mind control machines to make Carol Danvers love him, ends up aging to dust after returning to his home dimension due to being out of sync with its time stream. Carol returns to Earth and reams out the Avengers for letting him take her.
The Ultimate Marvel version of Deadpool was a major Scrappy amongst fans due to being a clichéd, mutant-hater rather than the unique, fun-loving Jerk with a Heart of Gold that Mainstream Deadpool is. Years later in Deadpool Kills Deadpool, Ultimate Deadpool is amongst the evil versions of Wade that attack him. So of course we get to see Deadpool curb stomp him and then stab the bastard to death on-panel.
Back in the late 70s, the much-maligned H.E.R.B.I.E. from the 1978 Fantastic Four cartoon was added to the comics, only to be destroyed after being revealed as a sleeper agent sent by a villain called Doctor Sun. The character was reintroduced decades later and used in a more positive manner, however.
The Red Hulk was subject to being beaten up by Iron Man, Thor, the original Hulk, and nearly fell into a black hole while being trolled by Uatu the Watcher. Many fans were happy.
During the last arc of Runaways, Chase actually tells Klara, considered by many fans to be a Replacement Scrappy, to shut the fuck up.
Similarly, one of the tie-ins to Secret Empire had the HYDRACaptain America incarcerate Sally after a botched interview. To really rub it in, he mocked her while she was being dragged off by sarcastically saying that he was sure people on Twitter would be outraged to hear about her arrest, a clear nod to her controversial speech from the previous Civil War tie-in.
Secret Wars (2015): Final issue of Ghost Racers has Arcade, a character who earned himself a very large hatedom by being responsible for death and derailment of many fan-favorite characters in Avengers Arena and Avengers Undercover and getting away with it, having his eyes torn out and then being run over by every single one of the Spirits of Vengeance, reducing him to a bloody stain on the ground. Needless to say, it was very cathartic to watch.
Spider-Island was one big Take That! against infamous Spider-Man Replacement Scrappy, Creator's Pet (she's named after Joe Quesada's daughter), Satellite Love Interest, and all around Relationship Sue Carlie Cooper. While at first it seems like more of the same— Carlie gets to sleep with Peter Parker, she gets Spider-Powers while Mary Jane doesn't, and gets to be a "super awesome" fighter to complete the Character Shilling — she then gets her butt handed to her in a fight, turns into a giant spider with the rest of the hapless citizens of New York, and the day ends up saved largely by MJ who gets Spider-Powers without turning into a giant spider. The comic ends with a Peter and MJ Ship Tease of the highest order. On top of that, Peter forgets about Carlie's predicament, leaving her naked and embarrassed in the middle of New York. And then already rejoicing fandom cheered louder when they broke up right after this. It dives even further in the Superior Spider Man comic. She's the only one who realizes that Peter isn't Peter and goes to investigate. As she does, she discovers proof that Dr. Octopus has taken over Peter's mind. She vows to go to the Avengers... and gets kidnapped by the Green Goblin and transformed into Monster.
Amazing Spider-Man #11 has the present day Peter Parker slug the Superior Spider-Man in the face, then proceeds to humiliate him to get him to calm down and work together. All the while, Peter's admitting he's enjoying this bit.
An issue of Spider-Man 2099 has one of the Inheritors, Daemon, confront The Punisher 2099. The Punisher beats him down. With a baseball bat.
The "Welcome Home" variant cover for Amazing Spider-Man #13 has Spidey 2099 and Spider-Gwen pull Spidey and Silk apart.
In World War Hulk - Frontline, Sally Floyd (y'know, the one who made that speechnote During Civil War: Frontline, she interviewed Captain America and gave him a lengthy "The Reason You Suck" Speech where she suggested he was out of touch with modern Americans because he didn't do things like use social media or watch NASCAR races. Needless to say, readers took it very badly. to Captain America) gets roaring drunk and wanders into the middle of a mugging. She's rescued by Moon Knight, who then tells her that if he'd realized who she was beforehand, he wouldn't have bothered saving her.note Moon Knight hadn't taken part in the Civil War and neither side wanted him. That said, his heart was clearly with Cap and the anti-registration heroes.
Turner D. Century was a Moral Crusader villain whose gimmick was that things back in the early 1900's were better and trying to destroy all modern things that he saw as immoral. He was a victim in the Bar with No Name incident and was the only one that the writers did not regret killing. To further this, one of the other villains there mockingly asked Turner if he was called Gay Nineties Man.
Relationship Sue Carlie Cooper. While at first it seems like more of the same— Carlie gets to sleep with Peter Parker, she gets Spider-Powers while Mary Jane doesn't, and gets to be a "super awesome" fighter to complete the Character Shilling — she then gets her butt handed to her in a fight, turns into a giant spider with the rest of the hapless citizens of New York, and the day ends up saved largely by MJ who gets Spider-Powers without turning into a giant spider. The comic ends with a Peter and MJ Ship Tease of the highest order. On top of that, Peter forgets about Carlie's predicament, leaving her naked and embarrassed in the middle of New York. And then already rejoicing fandom cheered louder when they broke up right after this. It dives even further in the Superior Spider Man comic. She's the only one who realizes that Peter isn't Peter and goes to investigate. As she does, she discovers proof that Dr. Octopus has taken over Peter's mind. She vows to go to the Avengers... and gets kidnapped by the Green Goblin and transformed into Monster.