In The Dilgar War has warmaster Len'char, whose actions and political meddling make Jha'dur (whose body count of innocent is so high she's called Deathwalker) look sympathetic, especially as Jha'dur did what she did to save her people and just couldn't see a pacifistic solution while Len'char put such survival at serious risk. When Jha'dur finally crossed the Moral Event Horizon, her promise to not kill him no matter how much he begged for it is quite satisfying.
In Game Of Touhou, during the sack of Muenzuka, Seiga tries to escape from there, picking one of Tewi's ships. The crew considers her too treacherous to take on board and let her to drown.
Turnabout Storm has Ace Swift, the murder victim. He was an athlete that had rumors about him saying that he reached his victories by less-than-honest methods, which turn out to be true. He blackmailed every opponent that had a chance of beating him into dropping out of the race or hand victory to him so he could keep his victory streak untouched, and was willing to go as far as threatening the families of his competition to this end. In the end he's even more an asshole victim than anyone thought, as his attempt to kill his partner in crime when she (overwhelmed by guilt) decided to quit was the direct cause of his (accidental) death.
DJ Sagara becomes this in Metroid: Kamen Rider Generations. As Sagara is the avatar of the Helheim Forest and considering that he orchestrated the Helheim incident in Gaim's TV canon, Gandrayda gives him a Deadly Gaze that left him Taken for Granite. For Gandrayda, it was so satisfying to see Sagara being petrified all while having that agonized expression in his face states that he got what he had deserved.
The second victim, Pekoyama, ends up becoming this when it turns out that she tried to convince Kuzuryuu to kill Koizumi in revenge for Koizumi destroying evidence to protect the girl who killed Kuzuryuu's sister. Koizumi, who had considered Pekoyama a friend, feels shocked and betrayed after learning this.
Despair's Last Resort has the victims of the third chapter, Shigeru Kitagawa and Naomi Williams. The former wasn't well liked among most of the students, while the latter showed their true colors as a jerk in the same chapter. It doesn't help their case that the reason they died was when they tried to kill Shizuka, who overheard their plans to commit a double murder and wanted to talk them out of it, Shigeru ended up killing Naomi while he was killed by Shizuka. The only person who bothers to act sympathetic about their deaths is the one they tried to kill in the first place, as she didn't intend to do so in the first place.
Three Point Shot has Korekiyo Shinguuji. After Kokichi ends up giving him and Tenko each other's motive videos, Kiyo and Tenko meet up to exchange them, and during the meeting, Kiyo tries to kill Tenko. Unfortunately for Kiyo, Tenko is able to thwart his attempt on her life, and finishes him off when he threatens to kill her best friend, Himiko. When Shuichi reveals that Kokichi is indirectly responsible for the murder, Kokichi asks if anyone is sad that Kiyo is dead, then says that Kiyo deserved to die.
In Where Talent Goes To Die, the first victim, Shiro Kurogane, counts. He spends most of his limited screentime antagonizing the main protagonist, Kaori Miura, for defeating and humiliating him in a shogi match as a demonstration of her talent. Not long after their last encounter, in which Kurogane gives Miura a vicious "The Reason You Suck" Speech after she tries to apologize to him, Kurogane is found dead in the boys' bathroom, murdered in an attempt to escape from the killing game. Unlike many examples, his being an asshole didn't directly lead to his death- his killer knew about the bad blood between him and Miura and so decided to frame her for his death.
In Murder Most 'Orrible, every murder victim is a complete asshole. Investigator Joan Sanderson-Reeves thoroughly sympathises, having as an Assassin terminated the assholery of eighteen wastes of oxygen. But she still has to bring an unlicenced assassin in before the Watch do, so that the Guild can make her an offer....
In Gankona, Unnachgiebig, Unità, the homophobe is this to Germany and Japan. They would have beaten the absolute crap out of him for nearly raping their precious Italy had Italy not begged them to stop.
Professor Karkaroff in The Parselmouth of Gryffindor, who, as in canon, was still a ruthless, immoral Death Eater, just an unusually cowardly one in the face of Dementors. Lampshaded when Dumbledore acts concerned about the murder:
Dumbledore: “I mean to say that he has probably been viciously murdered.”
Hermione: “…Ah, erm, not to make light of any human life, but why do you particularly care?”
In Harry Potter and the Methods of Rationality Rita Skeeter is killed off by Professor Quirrell This occurs after she starts a slander campaign against Harry to further her career so no one really felt bad. According to word of God this was supposed to prove once and for all that Quirrell is evil and the author was horrified that people were rooting for the professor despite that it was a disproportionate response to an issue that Harry had already solved.
Hivefled has Lereal and Dualscar. Both undeniably douchebags (Lereal was a fundie whackjob whose over-optimistic faith was responsible for the deaths of two hundred children and Dualscar was a slave-taking privateer who tried to get his ex murdered), but it's still pretty hard to argue that they deserved what happened to them (both effectively got raped to death).
In WarboundWidow Vriska is captured by the Church and subsequently imprisoned and tortured, including being victim to an eye scream. However Vriska had previously spent her time desperately mimicking Mindfang via slavery and rampant mind control, so it's very hard to work up any sympathy for her.
Queen of All Oni: The first human character to die in the story is Lung — since he was a Smug Snake and spent his chapter torturing Jade in an attempt to break her to his will, no one was complaining when Right chased him through his own fortress and brutally killed him mere inches from his escape boat. One reviewer applauded it and called it justice.
Nor was anyone complaining when Jade killed Kaito, or later, Ikazuki — both being Oni who loyally served Tarakudo, and who betrayed Jade and treated her like crap (respectively).
In Wheel of Fortune, one of the fanfics in the Horseshoes and Hand Grenades world, Mei Shirakawa's parents get eaten by and maimed by Renenutet for being evil parents to Mei. Ros and Guil also get similar treatment for only thinking about lining their pockets and pretending to be Mei's friends.
The Vow: A mongoose bandit Haun kidnaps Lady Lianne in order to ransom her to her father and smacks her for deriding him defiantly. With these acts combined with his arrogance, the sadistic way used by Lord Shen to execute him leaves no one to miss him.
In the deleted (because of the subject matter) work Pattycakes it is revealed that Rainbow Dash is one for not only having participated in the bullying of Fluttershy as a filly and only standing up for her to look good, but also emotionally and physically abusing Scootaloo. After all that, it's very hard to feel sympathy for Dash in this fic, despite the fact that's she's essentially kidnapped and psychologically tortured until she devolves into a child-like mindset and develops Stockholm Syndrome for her captor.
A Growing Affection: Danzo doesn't play a huge role, but when he does, he tries to subvert Tsunade or otherwise acts like a jerk. He gets framed as Gouki's mole and ends up dying saving Tsunade from the real mole.
Most of Naruto's victims in Demon's Dirty Dreams are either people who regularly put him down, stole from him, or tried to get him arrested. Thus, when he thinks back on having had sex with an unconscious Hinata, he feels like crap and decides to do something nice for her.
In This Bites!, several Marines come across the bound and Mugged for Disguise Inspector Shepherd during the Straw Hats infiltration of the base. None of them ever let him out of the closet he's stuffed in.
A New Chance Series has Rico. He not only did he successfully and brutally rob Jessie and James in this story he also sold Larvitar's mother to Team Magma, and after his defeat he bragged about it and then tried to kill Ash out of spite. Latios murders him behind Ash's back and sleeps like a baby afterward. It's deconstructed since Officer Jenny witnessed it, and regardless of how evil the victim was, the act is something a police officer can't ignore, which could have gotten Ash and Latios both in serious trouble...had his old friend Skailyn not used one of her servants to alter Jenny's mind.
Symbiosis has Damian and his friends. Damian was bragging that he abandoned his Charmander to die. When Ash catches him and Misty and Brock nearly gets Damian arrested, Damian planned to kill Ash to teach them a lesson. Fortunately, Pikachu overheard and decided to test hisnew moveon him...
A posthumous character, Amos, the previous sheriff of Dirt, was killed when Rattlesnake Jake injected venom into him, making him die slowly. Amos doesn't get much sympathy for this because before his death, he openly showed contempt toward Jake's abused mother and killed her while she was dying due to one of her husband's domestic beatings while having the gall to say it was merciful.
Another posthumous example: Jake's memories reveal that after he dragged away Tortoise John at the end of the movie, he tortured the corrupt mayor for days before ending him with venom as well.
The estranged husband of Grace Glossy, Benjamin Hares, left his pregnant wife penniless to escape his debts. He returns ten years later just to sell Grace's property in order to save his own hide again. When Grace tries to throw him out for good, he starts hitting her, actually relishing in it. Jake beats him up in return before injecting into him all the venom his fangs can provide, and no-one grieves over the coward's death.
A third posthumous example: shortly after his mother's death, Jake was caught in a rattlesnake round-up where he witnessed a human taking sadistic pleasure in skinning and toying with the snakes. Before escaping, little Jake made his first kill by using all his venom in the man.
Then, in Act II, when it's discovered that Miyabi raped Mizore, Dark goes ballistic and makes him pay for it in the most brutal manner possible by slowly crushing the bones in his arms and legs to powder before ripping them off, punching him in the face so hard that his jawbone snaps clean off, and finally ripping his spine out of his body with his bare hands. As shocked as they are by Dark's brutality, Tsukune and the others nevertheless have No Sympathy for Miyabi and unanimously agree that he deserved every last second of the beating.
Halla Peddle, the housekeeper of House Raylan has been reviled in and out of universe for the heavy physical and psychological abuse through which she put the servants under her command. No one legitimately mourns her passing when she is murdered by Wolfius and Kersea.
Rodrik Stone has been an unrepentant Jerkass and Hero Killer from start to finish of his lifetime in the story. In the end, he is killed by his intended victim, simply because he could not give up on his revenge towards her.
Prison Island Break: Silver was sent to prison for killing someone who will later rape and kill a bus full of children.
In Severe Misery, Sally Acorn, Bunnie Rabbot, Fiona Fox, and Nicole Lynx are meant to be seen as this, having been written as sadistic Alpha Bitches. But considering that the author's Self Insert character had arranged for them to be murdered by a demon dog over having been mean to her one time and then later vandalizes their memorial wall without getting caught, it makes her look much worse and the attempt falls flat.