LadyDevimon from Digimon Adventure was thrown in, apparently at the last minute, as one of these. The only reason for this, however, appeared to be to set up an Evil Counterpart with whom Angewomon could have a Cat Fight, complete with slapping and hair-pulling. They even brought her back in Digimon Adventure 02 just to repeat the process.
Karinka from Steel Angel Kurumi toes the line. She beats another main character, and lives primarily so she can destroy the main character and steal her boyfriend. Oh, yeah, she curses like a sailor, too.
A brief glimpse of Caerula Sanguis' distant past in Volume 9 of Battle Angel Alita: Last Order shows that when she was part of the Chinese Triads, she was very much an example of this trope. After meeting Victor Byron, however, she softens a little. She softens further after meeting John Farrell in Volume 8, to the point that she became something of a Hero Secret Service, at first against Victor, to protect John Farrell's grandson, Arthur, eventually extending her protection to the whole of humanity.
Naruto has a load of bait-and-switch Dark Action Girls who sometimes don't live up to their initial posturing or pull a whiplash-inducing High Heel-Face Turn, but the standout is Tayuya, the flute-playing, Sir Swears-a-Lot genjutsu expert of the Sound Four, who easily cows her Ax-Crazy coworkers, punches out the eponymous hero, and demonstrates, perhaps better than anyone in the series, save Uchiha Itachi, why genjutsu is NOT the "soft" one of the three main ninja skill sets. She then goes toe to toe with Shikamaru, the smartest guy in the whole series, and proceeds to back him into a corner and break his nigh-unbreakable binding jutsu with sheer brute force and bloody-mindedness. The only thing that stops her is having a forest dropped on her courtesy of Temari, a BadassAction Girl whose idea of a "cat fight" is breaking her opponent's spine and then tossing them across the room.
Balalaika was also one before she graduated to The Baroness.
Come to think of it, every major female character in Roanapur is a variant of this theme.
It's debatable whether Roberta (as of the anime) actually outdarks Revy. Her motives are selfless, after all: Give. Me. My. Morality Pet. Back. Now. SAFE. Until El Baile De La Muerte arc; if you thought Roberta was scary before... This is remarked on by the appearance of Fabiola Iglesias, the Action Girl and Badass Adorable who replaces Roberta as Garcia's caretaker and serves as her Foil.
Nena Trinity from Gundam 00, though she's more of a Dark Female Gundam Pilot.
Considering that Nena has only actually been able to kill stationary (like the wedding) or otherwise helpless (like Wang's shuttle) targets, she could actually qualify as a Faux Action Girl rather than a Dark Action Girl. The fact that Louise eventually kills her in a brutally one-sided fight certainly doesn't help matters. Even moreso, Throne Drei is built specifically for stealth and support purposes, therefore, asking it to actually kick ass is like sending in a squishycleric to deal with tough enemies that can deal a lot of damage.
Also, we may be able to include Soma Peries and Louise Halevy (from the second season on).
Hilling Care definitely qualifies for this, both inside and outside of a mobile suit. She technically lost against the 00 Raiser, but she did put up a big fight.
Subverted with As Nodt, whom everyone thought s/he was a girl but was later confirmedto be a dude.
Yachiru Unohana was one of these way back in the day. She was Soul Society's most brutal fighter and even today she is widely feared as Soul Society's most infamous criminal. The only reason she wasn't executed was because Soul Society wanted her on their side.
GUN×SWORD's Fasalina, who (unlike the only other girl in her group, Melissa, who was merely confused) fully embraced the methods of The Claw and, most of the time, puts up a damn good fight against the heroes.
One Piece has its fair share, from Miss Double Finger (and arguably Miss Merry Christmas) to Kalifa. Boa Hancock initially appeared to be this, but mellowed out over time (though she can still be cruel to enemies). The sole female member of the Blackbeard Pirates, Catarina Devon, counts.
Sabrina and Lorelei of Pokémon Special. Interestingly enough, both of them have joined forces with the protagonists at some point due to an Enemy Mine situation; in fact, Sabrina does so against Lorelei.
Arguably, Karen also qualifies. She's also a Dark-type specialist, to hammer the point home.
Pokémon - Jessie, especially when someone crosses or insults her. Her rival Cassidy also qualifies.
Ophelia: as a complete lunatic, obsessed with taking lives, she even kills her own fellow Claymores. She would have killed Claire if Irene hadn't intervened, which lead Ophelia to beg her dearly departed brother to protect her, while alone in the woods, and then moving to a hateful and (at least in the anime version) profanity-flooded monologue that ended with three F-bombs before "awakening". She makes BioShock's Sandar Cohen seem at least somewhat sane.
Any of the Sailor Animamates from the last series of Sailor Moon. Sailor Animamates were the servants of Big Bad Sailor Galaxia, who was hunting down Star Seeds/Sailor Crystals across the universe. They were all once good, but Sailor Senshi become evil when they lose their Sailor Crystals.
The Doom and Gloom Girls, Queen Beryl's last and strongest warriors from the anime, who very nearly succeeded in defeating the Sailor Senshi.
Also the Ayakashi Sisters, Evil Counterparts of the Inner Senshi and pretty competent combatants. In the anime, however, they have a collective Heel-Face Turn.
Esmeraude, as well.
Gavrill Madaraki from Franken Fran, the almost-invincible shapeshifting leader of an army of pillaging thugs.
Annie Leonhardt of Attack on Titan has shades of this, being a cold and cynical soldier who enlists in the infamously corrupt Military Police Brigade, abandoning her Fire-Forged Friends without a second thought. She's also one of the Titan Shifter spies, and her rampage as the Female Titan leaves scores of veteran soldiers dead. She turns out to be a more complicated case, hinted to be a Broken Bird with serious Daddy Issues. Word of God explicitly states she isn't inherently evil, though it's hard to deny that she's a Sadist that likes to get.....creative with her kills. When Eren and Armin attempt to talk to her, she goes on one final city-smashing rampage before encasing herself in a Crystal Prison, denying the military the chance to learn her secrets.
N'rala/Nurara from "Captain Future"...as far as the zeitgeist allowed it. (The Captain once floored her with a karate chop and commented "You're just a woman after all".)
Lady Shiva is generally regarded as the deadliest martial artist in The DCU. When Matt Thorne, the Crime Doctor, is on the run from the criminals he has betrayed, he asks for sanctuary from Oracle and her team. Injured and hurt, Thorne sees Shiva and remarks "Holy Mother of God. I'm almost honored they sent her to kill me."
Rose Wilson, aka Ravager of the Teen Titans, is the most badass girl they've had on the roster. Previously, she worked for Deathstrokethe Terminator, one of the DCU's top assassins (and also her father), though she eventually realized how messed up her relationship with him was.
Marvel's Titania is a foe of She-Hulk, and has similar degrees of superhuman strength and endurance.
Scandal from Villains United and Secret Six first appears to simply be a Middle Management Mook. However, she's shown to be extremely dangerous in combat, quite possibly insane, and very hard to kill (and it's revealed that her father is the immortal supervillain Vandal Savage).
Black Cat, one of Spider-Man's love interests. Her Heel-Face Turn is often a Batman Gambit, her betrayals less an indication of her turn than the prime motivator all along. Though she doesn't need love in her life, she can appreciate it when it's there and remembers it fondly after abandoning it, which is why she doesn't return to the Heel-Face Revolving Door by whacking the Hero.
The X-Men villain Mystique. Though her powers don't offer any real advantage in a fight, she's a skilled martial artist who supplements her physical prowess with an arsenal of firearms. She frequently makes fake Heel Face Turns that turn out to be Batman Gambits to screw the X-Men over, and when she betrays them, she naturally shoots or beats the shit out of whichever X-Man she'd gotten especially close to while she was "good" (See Iceman. And Forge, twice.). Somehow they always fall for it, because she's just that good at deceiving and manipulating people.
Mariah from Sin City. She mostly appears in Hell And Back as a deadly assassin who has a rivalry with vampish Blue Eyes, also a part of the same guild.
In Action Pack the only villains to appear as of now are women, Joystick , Iron Maiden, Snapdragon, and Quake. Both Joystick and Iron Maiden actually get one over on Spider-Man and they both get Black Fox to let them go, and coincidentally it takes both of them to take them down. And though only one actual appearance, Quake still goes head to head with Kira and can hold her own. The only real let down, the 'Faux Dark Action Girl' is Snapdragon.
Victoria Kati Ahart starts out as one in the Star Trek fanfic Safe and Sound, being one of Khan's followers and all, but she gets better as the story goes on. By extension the other woman follower, Cleopatra Suzette Ling, is most likely one too, but doesn't get the chance to show off her skills like Victoria does.
Stalker Fang is at least as much of a bad girl. Being horribly crippled then turned into Brain in a Jar inside a Killer Robot chassis can do that to someone.
Angelina, supposedly reformed murderess turned Special Corp agent/wife of 'Slippery Jim' DiGriz. Always carries an arsenal of lethal weaponry on her person, and has the ability to produce a .75 calibre recoilless from Hammer Space whenever she thinks her husband is getting too slippery for her taste. Supposedly, her more psychopathic impulses have been removed by the psych-techs, but Jim frequently has to restrain her natural enthusiasm for killing and torture.
Rare heroic example: Rachel from Animorphs, who begins as an Action Girl but gets closer and closer to this trope as the series goes on. Taylor could be seen as an actual villainous example, though she generally avoids using her unique fighting skills in favor of psychological manipulation.
Phrygiar Navaris from the Codex Alera is a psychotically obsessive swordswoman and one of the top five blades in her civilization - she normally hires herself out as a mercenary, and has racked up a kill count in the hundreds during her life (and those are just the ones we know about). Aquitainus Invidia from the same series is more like The Vamp, The Chessmaster, and the Reliable Traitor all in one person, but she's more than capable of getting her hands dirty if she has to.
Miss Hakkendottir from the steampunky The Hunchback Assignments: beautiful, thoroughly evil, and considers Mooks a disposable/consumable resource. Extra points for her two half-mechanical attack dogs...
Female Careers from the The Hunger Games series, which include Clove from the first book, and Cashmere and Enobaria from Catching Fire. Enobaria in particular even had her teeth sharpened to a point after ripping out someone's throat with her teeth in the Games she won.
Dime Novel hero Nick Carter had quite a few of these. Perhaps the most dangerous was Dazaar the Arch Fiend. Her specialty was knife throwing; she could throw a knife hundreds of yards with extreme accuracy.
Another of Dime Novel hero Nick Carter's female enemies was Zanoni the Woman Wizard, a skilled hypnotist and chemist (poisons were her specialty). She was a truly nasty piece of work.Once, after being captured by Nick, he warns her not to try to "make love" to him as a way to get out. Her reply conveys her fiendishness: "Have no fear, my pretty man, my cornucopia of driveling goodness. When I make love to you, it will be to your articulated skeleton—to your empty, fleshless skull—to your heart preserved in alcohol and your liver thrown to the dogs."
Live Action TV
Sarah Corvis in Bionic Woman reboot is to be a prime example. She teaches the Action Girl protagonist just so that she can fight her later. Sarah also seems to like to drop hints, though it's been shown she does have a motivating romantic interest.
Faith is half this, half Dark Magical Girl. Her abilities are action-based, not magical, and the fights between Buffy and Faith are adrenaline-spiked highlights among the series' many action sequences. Directors, stunt directors, actresses, and stunt doubles always seemed to go all out whenever one of these scenes came up. At the same time, her issues are much more of the DMG vein, and she is eventually redeemed DMG-style in a two-part episode of Angel. However, even after Faith returns and joins up with Buffy, the two constantly butt heads, often violently.
Darla. While in flashbacks, she's less action-y and more just plain evil, during the first season, she was The Master's Dragon. That is, until she died.
Callisto, Xena's Evil Counterpart from Xena: Warrior Princess. She does pull a Heel-Face Turn later in the show's run, actually. It takes divine intervention, though. It requires Xena — who, at this point, had died and become an Archangel — to take on all of Callisto's sins and suffering, thus damning herself to Hell for All Eternity. This removes all of Callisto's memories of being evil, which, not coincidentally, leaves her with more or less no memory of her life after turning twelve.
The lion goddess Sekhmet in Egyptian Mythology. She also was given titles such as the "(One) Before Whom Evil Trembles", "Mistress of Dread", "Lady of Slaughter" and "She Who Mauls". In a myth about the end of Ra's rule on the earth, Ra sends Sekhmet to destroy mortals who conspired against him. Sekhmet's blood-lust was not quelled at the end of battle and led to her destroying almost all of humanity, so Ra poured out beer dyed with red ochre or hematite so that it resembled blood. Mistaking the beer for blood, she became so drunk that she gave up the slaughter and returned peacefully to Ra.
Silencia Venemosa in Dino Attack RPG was a ruthless bounty hunter who single-handedly ruined two major corporations by foiling a heist on one, a sequence of events that resulted in the deaths of four small-time criminals, both CE Os, and at least two innocent bystanders (though neither actually died by her hand). The untold story of what she did at Dacta Corporation is said to be even worse.
There's also Lady Malys, also of the Dark Eldar, who goes for more of the "Dark Lady of War" approach. She's been compared to a Magical Girl anime villain, razor-edged steel fan and all.
Also, while wyches are not exclusively female, a majority of them are. The Dark Eldar value skill and potential above all else, so there are virtually no gender barriers. That also means that the Dark Eldar can hold this trope to every career path, from Haemonculus to Incubus to Archon.
Pathfinder has Szuriel, Seraph of Devastation, and Horseman of War. Once a fallen paladin, she now represents all of war's worst aspects, and of all the evil female deities is the one who most frequently gets physical.
The Witch from Into the Woods placed a curse on The Hero and his wife before the events of the show, practically abused her daughter, Rapunzel, by locking her in a tower for years, and cut off Rapunzel's hair and banished her into the desert. While the Witch had to work with the heroes for a time, she was the first cast member to start taking initiative when the Bigger Bad started killing everyone, and was dead set on sacrificing Jack to the Giantess. Then, towards the end of the show, she curses the heroes when they all confront her, throws away her magical beans, and vanishes, possibly committing suicide. And on top of all that, she's got attitude.
She is, however, one of the more sympathetic versions of this trope: She apparently really did care for Rapunzel, despite having no idea how to properly raise her, and is devastated (and sees her attempts to keep her away from the prince confirmed as correct) when Rapunzel is trampled on by the giant's wife, killing her.
Lynette Fromme and Sara Jane More in Assassins. The title of the play makes it rather obvious as to why these two ladies fit the trope.
Lucidique from Tortured Souls. Notable in that she starts out as a more standard Action Girl, going from an idealistic young woman who wants to save Primoridum from its corrupt ruler, to a vengeful, inhuman Anti-Hero who'll slaughter anyone who so much as annoys her.
Sylvanas Windrunner is THE dark action girl. Banshee Queen, Dark Queen of the Forsaken, Dark Ranger...she's basically a Dark Lord who just happens to work for the Horde, although Garrosh sees it in action in Silverpine when she raises new Forsaken from the Alliance dead.
Jaina Proudmoore, after the gigantic amount of Break the CutieMists expansion dropped on her. She is a Nominal Hero as Sylvanas is, and just so happens to rule an entire city of mages. The only thing stopping her from unleashing hell so far is Love Interest Kalec and the orders of King Varian.
She partially evolves beyond this in her chapter of the game, mainly because the swarm is fleshed out more giving her more people to interact with. Very much keeps the "Action" part, though - it's a rare mission she doesn't personally involve herself in.
Beatrix, the general of Alexandria, is one for most of the first two discs of Final Fantasy IX. Anytime she's fought by the party, it's a Hopeless Boss Fight. Lani the bounty hunter takes over for the rest of the game.
Larxene of Kingdom Hearts: Chain of Memories certainly fits the bill. She's well aware of it, too - her personal title is "The Savage Nymph", and she delights in taunting the heroes with "clues" that turn out to be completely fake. Plus, in RE:CoM, she manages to martial-arts kick Sora to the ground...TWICE. She's an absolute bitch to fight and, well, a bitch in general too!
The Fire Emblem series has always granted us with lots of heroic Action Girls. Likewise, there's usually at least one badass female villain in each game. And just as the female heroes in this franchise are typically exceptionally heroic, the villainesses tend to be absolutely vicious.
Hilda, Deet'var, Pamela, Eng, Maybell, and Bleg from Fire Emblem Jugdral. Especially Hilda, who's quite possibly one of the most evil villains in Fire Emblem history.
Ashera from Fire Emblem: Radiant Dawn is arguably even more of one then Petrine, considering she's an evil goddess who's really fucking hard to beat.
Aversa in Fire Emblem Awakening. Beautiful, Badass, elegant, exotic, seductive, and downright merciless, this lady is truly a FE Dark Action Girl if there ever was one. It also helps her case that she's REALLY hard to kill. She and the other villains survive, and if you play your cards right, she will join your party near the end of the game.
In the same game, the dark mage Tharja somewhat counts as a non-villainous example. With all her... eccentricities, she is still the darkest of the female good guys in the game.
In fact, every female opponent in No More Heroes probably qualifies under this trope, especially Bad Girl.
After being killed, corrupted, and resurrected in undeath, Sylvanas Windrunner slips easily into this role. Unusually, she's often portrayed with sympathy (depending on your interpretation, she could easily be considered a protagonist), and actually doesn't like her new role very much. Indeed, the only things that seems 'dark' about her are her fighting method and aloof personality, not her goal (which seemed...nice).
It is heavily implied that Nathyrra of Neverwinter Nights: Hordes of the Underdark used to be one. Almost every female drow that shows up in the campaign, as well as Aribeth in the original after her Face-Heel Turn and if you keep her on the dark side in Hordes of the Underdark, also qualify.
Bodhi from Baldur's Gate II: Shadows of Amn. Even if your PC is a heavily armoured warrior with an Infinity+1 Sword or two, she can probably wipe the floor with him or her in single combat with her bare hands, while wearing less than required by decency.
Simply because playable characters are almost automatically good at combat, any evil female Player Character is bound to count too, unless particularly inept in combat, as is any evil female group member, which actually only includes Shar-Teel and Viconia.
Tavion and Alora from the Jedi Knight sequels. Both are dark jedi and (sub-)bosses.
Tati from Rise Of The Kasai, while not really a villain, qualifies for this trope. She's absolutely vicious and won't hesitate to kill any Kasai warrior she sees. Her family was slaughtered by the Kasai, she once hung out with her era's equivalent of a street gang, and she's cursed with a mark that is gradually corrupting her. She hates the world for this curse as well. Hatred runs through her veins.
Sasha from inFAMOUS would also fit this trope. She was formerly Cole's (or, moreaccurately, Kessler's) girlfriend, and she's also one of the boss encounters in the game.
In Vampire: The Masquerade – Bloodlines, if your character is female, Mercurio says something about not wanting to speak of some matters (a vampire being a slut) in front of a lady. Your response is that a knee to the crotch tends to get men talking. He immediately talks.
Jack of Mass Effect 2, a shaven and tattooed biotics experiment, whose experiences have left her unstable, to say the least...though traveling with Paragon Shepard can make her a bit more balanced and less sociopathic.
This can be applied to a female Commander Shepard, as well, if you choose Renegade options in the game.
Kat in Halo: Reach is a case of a Dark Action Girl in the protagonist's team. This doesn't make her exactly "good", however.
Selvaria Bles in Valkyria Chronicles. She is practically invincible, and she has zero interest in serving anyone else but the Big Bad, Maximillian. Her virtue, however, is due to loyalty, not due to for sheer lulz and evil.
The female Imperfects would definitely fit here in this trope. Solara incinerates people, Fault Zone loves to make the ground tremble with her seismic accelerators, and The Wink seductively slashes people. All three are fueled by hatred and vengeance, just like their male comrades, Brigade, Hazmat, and Johnny Ohm.
And then there's the killing machine, Paragon, though she's not really one of the Imperfects.
Also, Cammy and the Dolls used to be Dark Action Girls, as Bison's brainwashedBodyguard Babes. Cammy has a full Heel-Face Turn once her inner humanity is unlocked. In the case of the other Dolls, however, it's not that easy: they suffer heavy physical and mental consequences, and at least one of them (Julia a.k.a. Juli) has become an Empty Shell due to it. (Though another, Juni, is in her path to recovery after waking up from a coma, so not all hopes are lost.)
Crimson Viper seems to fit in as well. Subverted, actually: she's a genuine Action Girlposing as a Dark Action Girl. While cold to the other warriors, she still has a kinder side that she shows to her daughter Lauren.
The Soul Series has a few. Tira is the best example, completely insane and just loves to kill. She also killed Sophitia and corrupted her daugher Phyrra into the local Dark Magical Girl. Ivy is one but on the good side... just a good side that doesn't care about all the other good sides.
From Tekken, we have Anna and Nina Williams, both assassins.
Rider of Fate/stay night embraces this image, although she does show a nice side — how much depends on the scenario. Her alignment is Chaotic Good. I guess you don't have to be evil to be a Dark Action Girl, though.
In Homestuck, thirteen year old Vriska Serket is an murdering egomaniac- the most violent, sadistic, and remorseless of all the trolls and is considered evil even by the standards of her barbaric planet. She is responsible for the deaths of thousands of trolls, as well as a teammate, and for seriously crippling two of her "friends" (and later killing one). She also purposefully facilitated a chain of events that led to an indestructible demon to be created and kill many, many more people- just because she wanted to have the glory of killing said demon. She's also among the most powerful characters in the comic. Later, however, she begins to realize that her upbringing was what caused her to become like this, as she was forced to hunt other trolls to sate the hunger of her spider-monster custodian, under threat of death. For the first time, she also feels true remorse after killing one of her friends. Her contact with and romantic interest inJohn also helps her see the error in many of the things that she's done. However, just as she comes to the conclusion that she doesn't want to kill or hurt people anymore, she is killed by Terezi in order to save the remaining trolls, as her plan to fight Jack Noir would have resulted in their deaths. As a consequence she has become one of the most controversial characters in the fandom. Later, we encounter Vriska in a dream bubble two years after her death. She's changed quite a bit.
Meenah Peixes is the Dark Action Girl for the pre-scratch trolls. She greets people by trying to kill them and is indirectly responsible for a few deaths in her team (even though she had no intention of causing them). She also idolizes her post-scratch counterpart, who is a genocidal tyrant. She's not anywhere near as bloodthirsty as Vriska was, although just as egotistical and belligerent, and a lot more mischievous. Needless to say, when the two meet, sparks fly.
Because almost every female cast member of Homestuck is an Action Girl in some sense, essentially all female antagonists in Homestuck count as this.
Considering that until, Agatha freed the other Jaegers, she was doing pretty well holding her own against guards and Othar, Jenka from Girl Genius likely qualifies. Mamma Gkika, being one of the Jager Generals, probably falls somewhere between this and Lady of War. Von Pinn is just Ax-Crazy. And then there's Dupree, who's axe CRAZIER. She routinely attempts to murder entire towns (and, it's implied, only fails because her commanders won't let her) and actively taunts Von Pinn, who can tear Jagers apart with her bare hands.
Lifolei (which is on the 'good' guys side!) and Thlassa of Juathuur.
Kusari from Sluggy Freelance - a masked assassin with superhuman powers who unfailingly follows the orders of the villainous Hereti-Corp executives. Her perhaps even more dangerous "sister", Oasis, is too nuts to count, especially as she imagines she's actually good.
Sakido from Slightly Damned certainly had a history as one of these. She was one of hell's most elite warriors in The Great War before retiring to the ring of the slightly damned. She shows us what she's made of when she takes down the guardian of hell and then single handedly fights her way through the legions of demons to get her little brother and his friend Rhea to the mortal world, even though she knows she'll die in the process. Doubles as a Crowning Momentof Heartwarming
Lazuli plays the role much straighter, and is pretty terrifying.
Pretty Pink Ponytails in Angel Of Death is a highly skilled, sadistic, and unstable fighter. Thus far, she's the only human to survive direct combat with Cody, and the only reason she didn't win is because he, who has super strength and speed and the ability to fire bursta of magical energy from his hand, called the police on a mortal.
A recurring character from v2 to v4 of Open Blue was Kapitänin Karla Weir. She worked for a 19th-century equivalent of Nazi Germany, was rumored to perform raids on colonies belonging to fellow member states of The Federation, and was frequently called on by intelligence officer and literal baroness Rhianna von Adolph to help her with carrying out the occasional dirty work.
Rhianna herself qualifies, being a highly-skilled Knife Nut armed with a diamond-coated combat knife. Unlike Karla, she makes a comeback in v5, if only reduced to a backstory role.
Tex in Red vs. Blue is not only the only woman in blood gulch (until much later), but also the only capable soldier. She's technically on the side of the Blue Team, which doesn't stop her from abusing and scaring the shit out of her allies. She is also the one character who wears black armor.
A fair amount of villains in Survival of the Fittest fit this, on at least two occasions, being a homage to Mitsuko Souma. Examples include Angelina Kaige (v1), Mariavel Varella (v2), Melina Frost (v3), Clio Gabriella (v4), Reiko Ishida, prior to Character Development (v4), and countless others.
Silver Sable from The Spectacular Spider-Man, an incredibly dangerous and clever combatant who serves as The Dragon to her father, mob boss Silvermane. Black Cat from the same series might also be considered an example, though, being something of a Catwoman figure, she's sometimes antagonistic but not exactly evil.
Averted in most of the movie, considering that nobody is even aware the Phantasm is female until the final act.
Magica de Spell from DuckTales, an evil witch that desires to steal Scrooge McDuck's first dime so that she can cast a spell to make herself rich.
Inque from Batman Beyond. In addition to being a really effective, if not, really badass shapeshifting blob, she's the embodiment of implacable. Frozen, diluted, and dissolved, in that order, all things that would assuredly damage or kill her and is STILL alive. On top of that, all of her encounters with Batman are usually with her cornering or nearly killing him. She even manages to nearly off Bruce Wayne in steroid armor. The only appearance in which she's not a major threat, it's because the "Innocent Bystander" she takes hostage is actuallySuperman.
Lazerette and Cerina from Skysurfer Strike Force. Cerina especially doesn't get in the thick of it as much of the other Bioborgs, and has no visible powers and rarely uses weapons, but she still gives the Skysurfers more they can handle when she does fight.
In the Mega Man cartoon, Doris the maid, a cosmetics robot, Ms. Lapierre, and a brainwashed Evelyn Ray have all fought Mega Man and Roll at points. The park attendant from Fun World was also evil, but she didn't fight.