Ashley in 72 Hours starts out as this before her HeelFace Turn. Like many other students, she's just trying to stay alive, though unlike the overtly Technical Pacifist students, she has no qualms with killing. Indeed, she has an innate streak for sadism and is intent on destroying SABRE from within. Luckily for them, however, her infiltration efforts lead her to realise that she's on the wrong side, and she becomes one of their greatest assets in the end. Not to mention, she winds up the only character who ends the book alive.
Numbuh 86, along with the rest of the Decommissioning Squad, oddly enough were given the Anti-Villian treatment in Operation:REBEL In the story, they seek to capture and Decommission a trio of 13-year-old KND Operatives who are looking for a group of anti-decommissioning rebels called the Kids Eternally There to seek protection from the Squad, the now teenaged Operatives honest don't see themselves wanting to betray the KND for any reason, but Numbuh 86 is worried that betrayal from escaped teen Operatives would be inevitable and strongly believes decommissioning the 13-year-old Operatives is the only way to assure that doesn't happen.
Sympathetic or not, it's undeniable that Aeon Natum Engel's version of the Migou got a valid point for justifying their war against humanity. Namely, about possibly causing a ruckus with their Arcanotech that will wake up certain cosmic horrors, Cthulhu included.
Played with in Dungeon Keeper Ami. The titular character is not a villain by any stretch of the imagination, as expected from one of the heroines from Sailor Moon. However, her goal of returning to her home dimension potentially endangers billions, by allowing the Dark Gods to follow her, and she refuses to be dissuaded. As such the Light reluctantly fights against her in several instances.
Of further note is Mukrezar. While unquestionably evil, it is a toss-up weather he actually counts as a villain, per se.
Zack Dawson, the main antagonist in Volume V of the supercrossover military fanfiction series The Terminators: Army of Legend, wants to achieve a peaceful utopia free of war and violence. Unfortunately, the only way he believes to achieve this unreachable goal is to waste any and all fortresses in his path, destroying all militaries throughout the world, with civilian casualties being considered as nameless martyrs in his noble cause.
In The Bridge, upon arriving in Equestria and being free from mind control by the Xilians, Monster X is shown to be a Noble Demon. He doesn't bat an eye at killing and is now part of the Big Bad's forces, but if he can manage it he will go out of his way to avoid harm coming to the defenseless.
In the Evangelion/Warhammer 40,000 crossover Thousand Shinji, Shinji is a manipulative jerkass, makes very questionable things... however his greatest desire is being loved, and he makes bad things to protect or avenge people he cares about.
In the end, all I really wanted was someone warm at my side at night. Is that such a terrible thing to wish for? To not be lonely like this, to know that when you go to sleep there will be someone who loves you waiting to smile at you in the morning? Is that too much to ask? I would trade it all just to have that again.
Dr. Moira Vahlen is this in Arad's Stardust. While she comes off, even In-Universe, as a JerkassMad Scientist, she does have valid concerns. Twilight Sparkle has so much telekinetic power she's like a walking A-bomb that can detonate multiple times, she can teleport practically anywhere at will, turn invisible and inaudible, perform spells that compel individuals to violently attempt to gain possession of a target she designates, and she seems to just keep coming up with new powers. A hostile Twilight Sparkle would be a nightmare to face. As proven in chapter 33.
Alternate Reincarnation is unclear about which type of anti-villain Kurumi belongs to (just like canon) but Rinne is largely Type IV, as in 'Villain in Name Only.' She does not have a single bad bone in her, actually serves as her friend's conscience at times, and even wishes to see Kurumi being redeemed if possible. Even her goal is simply to find out what connection does she and Shido have.
Light and Ryuk in A Charmed Life. Light really does want to make the worlds a better place and while Ryuk's sense of fun can have rather disastrous results Light concludes it's not done out of any purposeful malice but just because he doesn't know any better.
Fade: Thanks to knowing how he went Jumping Off the Slippery Slope in the story, Light resolves to never become like canon!Kira. He sticks to killing only people who have received the death penalty and/or have committed crimes that deserve such a punishment, does not kill anyone who stands in his way, and absolutely abhors the idea of using innocent people to further his own plans. He even refuses to sell out Near to L after figuring out that the former is the one who kills him in the story, as Near has yet to do anything deserving of that fate. While that doesn't change the fact that he is still a Serial Killer, it makes him more sympathetic as it seems he truly does want to make the world a better place. L, on the other hand...
Callidus Dominus from the Cynical Classicist DW Fanfics, such as Devotee of Augustus. He is quite aware that he is doing some morally ambiguous things, but justifies this in thinking that benevolent dictatorships are the best form of Government and sometimes gets the Doctor's assistance against greater threats, like the Daleks and Virmok Empire. This goes for other members of the Cult of Augustus and Malphan Empire.
From the same author is Professor Osmond Stone, from The Sleeping Survivors. While he is kidnapping people and putting them in suspended animation, he is doing it to save the human race, believing eventually an alien attack will destroy humanity.
Deadlock, the Big Bad of The Legend Of Spyro: A New Dawn. She didn't want to be evil and admits that she has her regrets. She's just lost everything, including her sanity, and feels that Spyro and Cynder are responsible for her tragic life, prompting her to attempt revenge. She also feels like her present plan is the only thing she hasn't tried in order to get something extremely important to her. On top of this, she's a very good queen to the Naga and treats them with respect, even being called the best queen they've ever had by some of them.
Game Theory does this with Precia Testarossa, who treats Fate considerably better and also explains her motives to both Fate and Nanoha. Add in a minor incident with Chrono and Nanoha is now working with Precia to help her achieve her goals. Fate is also a somewhat different Anti-Villain than she was in canon, given that her personality is still the same - she just has no reason to change sides.
Ballade turned out to be one, as he realized that being the robot Wily's most proud of meant others will fight for the spot, and while he showed respect to his enemies he got no respect from comrades. In the climax of episode 10 he sacrifices himself because continuing with the plan would endanger an innocent human life.
Mr. Black was revealed as this as more of his back story came to light, as well as his guilt and bad luck with the missions he's assigned.
Mega Man Reawakened has Woodman, who loves nature and tries to help Robert sort out his anger in the midst of battle.
It also has Glyde, as he turned to Wily out of having nowhere else to go and showed clear regrets over the matter.
In Bad Future Crusaders, Babs Seed is a good Royal Guard and believes in the law, but just so happens to work for the oppressive regime of a tyrant who rose to power in a coup.
Likewise with Crimson Sky, who's a decent family stallion and A Father to His Men, but not only serves Twilight, but also helped enable her coup in the first place.
Sweetie Belle seems to have become completely amoral, willing to make a deal with the people who killed her family, and not bothering to contact her oldest friends when finding out they're still alive. That being said, she's helped transform the Diamond Dogs from uncivilized brutes to a flourishing society that coexists peacefully with Equestria.
A Growing Affection: Gouki Namikaze wants to rule the world, and is willing to enslave (preferably) or kill (if required) all ninjas to do it. But he genuinely believes that he can make the world a better place. He treats his followers with kindness and respect. He loves his wife. And though he will kill if absolutely necessary, he prefers not to, unlike many of the 'good guys'.
ChasingTheShadow has Orochimaru and Kisame, both of whom, while vilainous in inclination, display and act on positive attributes with regard to their friends and comrades.
Brave New World: According to Richie, Light of Justice is a type III; a Nice Guy with a noble goal who wants to be Richie's best friend. He just happens to be a Knight Templar. Thus, it isn't surprising that he is the reincarnation of N, King of Team Plasma. Also, when the Light of Justice hears of the true extent of the Nihilator's crimes, he wants to put aside the gathering of Arceus' plates to focus on the Nihilator's destruction, and is certain that his organization and Team Getem can put aside their conflict to defeat an organization that is truly evil.
Pokémon Reset Bloodlines: The resident Knight of Cerebus, Belladonna Tyrian and her girlfriends are this. As Bloodliners, they consider themselves above humanity and thus have little regard for the law, but their typical actions are usually just breaking into places and theft, the sole exception being the events of Chapter 23, and even then they had standards. In the end, they're a group of lovers that typically act more like teenagers wanting to have fun, only going worse when someone harms one of them.
Like in canon, Emerald is loyal to Cinder (even more so here because theyre also lovers), but is horrified and conflicted by what Cinder makes her do.
Leonardo was already pretty sympathetic (or pathetic) in canon. Here, Salem is holding his wife and child captive, forcing him to help or shell have them killed painfully.
Vale's Underground: Hazel is the only criminal in the entire work with a sympathetic character and motivation. Yes, hes assisting an organ harvesting operation, but only so he can save his sickly and dying daughter.
RWBY: Dark: Yang Xiao Long never wanted to be evil, but had her mind broken and and twisted by Ruby, and will now kill at Ruby's command.
Harris Flowers. Despite his noble demeanor and trying to appear as friendly as possible, he is an unstable Control Freak who quickly resorts to violence when things don't go his way and who has problems controlling his urges. He is also a strong, generous and just leader with a natural talent for ruling. Ultimately, his goals are absolutely well-intentioned, but it doesn't change the fact that he is willing to murder others to achieve it.
Jaylon Gordus is a very tragic figure. A rude Jerkass of a man, he comes from a dysfunctional family, with a depressed and abusive father, from whom he ran away. Stranded in Oldtown, he long since realized that he is doomed to a life he does not want to lead, fighting for a man he does not want to fight for, but left with no alternatives. This turned him, once idealistic and proud, into a cynical jerk. However, he reveals his more likeable side when he temporarily joins up with Samantha to save Lucas, first out of necessity, but later on out of genuine affection for her and the others, showing that not all of his former self is lost.
In the Alternate Universe FicPrison Island Break, the protagonists are barely even Designated Heroes. Their goal to escape prison isn't particularly noble; all admit guilt, and most intend to commit more crimes on their escape. Their crimes include murder, rape, bank-robbery, fraud on a global scale (Tails claims to have nearly made himself the sole owner and stockholder of Sony), escaping other prisons, and what boils down to terrorism. It's the Morality Kitchen Sink. However, since the story is told mostly from their perspective, Sympathy for the Devil ensues to some degree.
In Black Wings, Black Sails, Laurence aims to free as many slaves as he can by capturing slaving ships and attacking slave ports. By Chapter 3, he winds up joining forces with the Tswana, after finding that many of the slaves he's rescued originate from their kingdom. Deplorable as the trade may be to us modern readers, it still supports a lot of livelihoods and all of the labor from the trade results in unprecedented agricultural productivity that drives the First Industrial Revolution. This contrast is underscored when Laurence slits a slaver's throat without remorse, prompting Granby's horrified reaction and remark that Laurence just killed a man in cold blood.
In the Anomaly (Series), John A. Pence is discovered to be this after it's revealed that the Anomaly was using him as a puppet, and in reality he had far less extreme goals before being hacked by the Anomaly to replace Frisk as the player character.
A running theme in Bird is the traditional Hero/Villain roles. In the world of Earth Bet Heroes and Villains work on principles of Grey and Grey Morality, with Villains being the Designated Antagonist role and not always unsympathetic, or even evil. This is subverted in Bird, where most of the patients at Alchemilla come from both sides of the fence but nearly all of them are sympathetic, and dangerous.