The eponymous Lupin IIIand his gang are the longest-running, most successful, and still one of the most popular examples of the trope. Whether it's the television series, or the annual Made-for-TV movies, the plot always centers on Lupin's pursuit of his next big score, with Inspector Zenigata always hot on his trail to slap the cuffs on 'em.
In the first anime series, Masaaki Osumi, the original director, made Lupin a cynical and morally ambiguous character that wouldn't hesitate to kill those who stand in his way, but tries to kill as less as possible to keep his family name reputation to the best. The first seven episodes reflect this as well, as the atmosphere is dark and mature with sometimes a melanchonic tone that hide a strong message.
In the first series, he murders a group of rival gang members by flooding their base with water, then threw high tension cables in the water, causing them a slow,painful death. In the second episode, he smirks while his rival in love Pycal burns to death.
As it turns out, Judge has this with Hiro and Hikari, too. He and Hikari created the Judge game as a sadistic Revenge by Proxy towards the jury and judge, who gave the drunk driver who ran over and killed Atsuya a milder sentence.
Lucy from Elfen Lied is a cold-blooded killer. She has killed armed men and innocent children, for reasons ranging from "trying to kill me" to "You killed my dog" to "I envy your happy, normal life, and I need a place to crash." She kicks people quite sadistically when they are down. She hears voices and tries to infest humans with her diclonius genes, which will lead to the extinction of mankind. No effort is spared to let the viewer feel sympathy for her plight, not even after sacrificing herself in the end, where it was only to save the one guy she liked - without ever learning that being a sadistic mass-murderer is wrong.
The main character of Fire Punch, Agni, straddles the line between this and antihero for much of the story. There are multiple arguable points where he crosses over the line into straight up villain, but the most definite moment would be when he murders a repentant Doma and all the children Doma is taking care of in the frozen wasteland that is the setting. Even though he is hit with a massive Heel Realization moments afterward, his slipping sanity causes him to do other terrible things as well.
Haruko Haraharu is very much the face of FLCL, acting as one of the premier Manic Pixie Dream Girls in all of media. Energetic, spontaneous and hammy as hell, but manipulative, selfish and ruthless, to the point where there's a distinct Lack of Empathy. She cements it by trying to feed Naota into the Terminal Core and endangering the Earth's existence out of her desire to absorb Amtosk's infinite power. By the end, however, she's mellowed out considerably. Or at least seen that shes lost this round.
The Pleiades Saints from Puella Magi Kazumi Magica are out to stop the witches... by kidnapping and cryogenically freezing them when they’re still magical girls. Also, many of the members of this organization end up turning against each other as well. Special mention goes to Kanna Hijiri, who ends up being the Final Boss.
Mireille Bouquet from Noir who never questions her job of killing people (although she's more Nominal Hero).
The very end of Katanagatari shows that Togamealways intended to sacrifice people, swords, friends, even her own feelings in a mindless pursuit for revenge. Period, end of story. She still genuinely loves Shichika, and she has a very good reason for her behavior, but she never managed to let go of her desire for Revenge Before Reason, to the point where she often goes against her very nature in order to achieve it.
Future Diary is interesting as the true protagonist is reasonably moral (though not truly heroic), but all of his allies seem to have rather questionable morals. One is a terrorist who thinks nothing of blowing up a school while it's occupied, while his closest ally and potential girlfriend is dangerous. Over the course of the series, he does eventually become more immoral and becomes as nutty as his girlfriend. Many characters call him out on his villainous behaviour as he gets worse and worse.
Tanaka Punie of Dai Mahou Touge is definitely not as good as her "princess of Magical Land" persona makes her appear to be. Her incantation says it all: "Lyrical Tokarev, kill them all!"
Yuuhi and Sami, the main duo of The Lucifer and Biscuit Hammer. Sami has vowed to destroy the Earth herself after saving it from the eponymous hammer, and Yuuhi is extremely loyal to her for that end. The other Knights besides Yuuhi don't know about Sami's intention; Yuuhi and Sami plot to turn against them as soon as the world is saved. After much Character Development for both of them, they get better. Yuuhi eventually 'defeats' Sami, who didn't really want to destroy the Earth at that point, and the two go on to live Happily Ever After.
Aur from Maou no Hajimekata is a cold and nefarious man, he made a point in his introduction that he absolutely loathes humanity and will do whatever it takes to make them bend over to his will through all kinds of evil Aur plans for them, throughout the series we see he wasn’t joking, he goes on to enact genocide, enslave human settlements, rape women to submission until they start liking it.
The protagonist, Ryo Narushima, in Shamo. He murders his parents in the first 3 pages of the book, and throughout the series commits (or at least attempts to commit) multiple acts of murder and rape.
Mayo Sasaki in Fushigi Yuugi: Eikoden. While she's not truly evil, she is extremely selfish and unsympathetic, and her obsession with stealing Miaka's beloved husband Taka/Tamahome, coupled with her irresponsible behavior, causes a lot of trouble for the warriors of Suzaku.
Yoshitaka, the male lead of He Is My Master is a sociopathic pervert with little to no redeeming qualities.
Mobile Suit Gundam SEED CE.73: Stargazer does this with the pilot of the Strike Noir, Sven Cal Vayan. He is the character with the most focus and the only one that (due to the length of the story) got any degree of backstory. He's also shown to be extremely cold, more than willing to gun down entire crowds of refugees on the off-chance that one is a terrorist, and shows no trace of remorse or grief when a wingman gets killed. He does eventually get better, but not before getting into a Chained Heat situation with the Hero Antagonist of the series and the pilot of the Stargazer.
The Count of Monte Cristo aka Edmond Dantes from Gankutsuou. Especially when the title monster is in control of him.
Alucard from Hellsing . The first anime leans towards Anti-Hero, but the manga and OVA series depict him as more of a self-declared monster: terrifying, vicious, and wholly in the business because he loves killing people.
This is especially prominent in the first four episodes, with Alucard's vicious slaughtering of both Millennium vampires AND an unfortunate Brazilian SWAT team that effectively got thrown at his mercy by corrupt police officials who were bribed by one of those vampires. However, to be fair, in the later episodes, Alucard's more sympathetic and redeeming qualities do come to light.
Ookami no Kuchi: Wolfsmund begins as a series of tragic stories only connected by the presence of sadistic bailiff Wolfram and the eponymous border pass that he oversees. Virtually no one has gotten past Wolfsmund alive or unscathed thanks to him. However, it eventually becomes clear that the story is really about the formation of the Old Swiss Confederacy; Wolfram himself is merely an embodiment of why the Swiss hate Habsburg rule so much, and ends up being a Decoy Protagonist who is executed 3/4s of the way through the story.
Sheila of Superior wants to achieve a future where humans will never again slaughter demons. However, she believes that the war will never end so long as both humans and demons continue to exist. Naturally, her solution is a bit . . . final. (Exa's near-absolute pacifism provides the jolt she needs to stop killing, at least temporarily, but matters aren't helped by the fact that she's the one person Exa wants to kill, as vengeance for slaughtering his entire village.)
Ling Xiaoyu from Tekken: Blood Vengeance is probably the most heroic example of this trope ever, seeing that she was only in it because her target is a hottie. After her opponent goes out of her way to save her life following a showdown, she pulls a Heel–Face Turn and allies herself with her so they can get to the bottom of what their superiors are really up to.
Natsuo of Teppu definitely qualifies. The realistic high school setting of the manga means that she's probably not going to be murdering anyone, but she has demonstrated herself to be ruthless, selfish, arrogant and frequently sadistic. For example, she initiates a fight with her future rival just because she's bored, and her rival's cheerfulness and self-confidence pisses her off. Natsuo has gotten a little less arrogant over the course of the series so far, but otherwise she's still just as much of a bitch as she was at the start.
In Black Lagoon almost all the main characters are villainous, and some arcs (like the first arc, and the initial Roberta arc) sees them take the actual villain's role by doing stuff like kidnapping, or doing stuff like supporting Balalaika, who is the Big Bad of the Yakuza arc (with the Washimine clan and Yukio being the closest thing to 'the hero', up until the point where The Bad Guy Wins).
In Canaan the main character Canaan is a gun-for-hire that kills mercilessly, even when her innocent soul mate Maria lays witness to her line of work. Albeit her cold personality is softened in Maria's presence.
Michio Yuki from MW. He is the main focus on the manga as he spends his time committing murder, not to mention collecting ransom money on his victims. He also crossdress women in his plot. His goal is to find MW and use it to end the world in vengeance for his own mortality.
While Kurosu in Ana Satsujin may not be a perfect example of this, he does count solely because of who his girlfriend is: Miyaichi, a not only unrepentant, but proud serial killer, who definitely does count. He counts because he finds this out before he decides to start dating her, and while not agreeing with her activities, doesn't do much to stop her and sticks with her after she starts roping him into helping her with her kills.
Two of the protagonists in Terror in Resonance are terrorists who are planting bombs all over Tokyo. Granted they aren't trying to actually kill anyone .
Afro from Afro Samurai practically embodies this trope; while he is always motivated by some narrow view of "justice," nearly every interaction he has with other characters including his own conscience makes it exceedingly clear that he is flat-out in the wrong when it comes to his killing sprees, which only serve to further throw off the balance of an already Crapsack World.
Michiko & Hatchin is about a woman who breaks out of jail and kidnaps the daughter of her old lover so she can lead them to him. Michiko and Hana develop a strong familial bond over the story but she still took her from her (abusive) foster parents and is on the run.
In Yu-Gi-Oh! The Dark Side of Dimensions, Seto Kaiba has become more antagonistic since the Pharaoh left, and the movie closely revolves around him. Most of the conflict in the movie is directly his fault, as he refuses to let anything stop him from dueling Atem.
Kasane's title character starts out as just a very desperate girl who wants to escape her crappy life by using the face of another woman to become an actress, but as her fame rises, and with Habuta's "help", she undergoes some serious Sanity Slippage. She completely breaks after her last Morality Chain, her little sister Nogiku, tries to betray her by exposing her secret.