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.
In Origin Story, a Buffy the Vampire Slayer / Power Girl crossover''. no one is mourning Bullseye too much after he's killed, even taking into account his brutal death at the hands of Alex Harris. In fact, at least one law enforcement authority expresses relief that the assassin is no longer going to be killing people, and another authority says that if there was anyone who deserved a good killing, it was Bullseye.
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, is 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.
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.
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 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 "currently now deleted" work Pattycakes because of the subject matter, it is revealed that Rainbow Dash is one having not only participated in the bullying of Fluttershy as a filly only standing up for her to look good, but also emotionally and physically abuses Scootaloo. After all that, it's very hard to feel sympathy for Dash in this fic. (Note: This was written during S1 before RD had all those Pet the Dog moments with Scootaloo and Fluttershy as well as Character Development.)
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.
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...
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.
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.