In the Babylon 5 fanfic 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.
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.
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).
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.
Prison Island Break: Silver was sent to prison for killing someone who will later rape and kill a bus full of children.
In the Discworld fanfic 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....
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).
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...
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.
Also Shadi Enigmar who sexually harassed a waitress and tries to beat her to death for failing to see Phoenix cheat at cards.
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.
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.
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.