Misa Amane from Death Note wears black more than once.
Utau Hoshina from Shugo Chara! is yet another subversion (moreover, she wears other outfits with other colors as well). She's just a little too willing to do bad things to save Ikuto from his commitment to Easter.
From the same 'Verse, the merciless Space Pirate Queen Emeraldas is a straight example.
Haman Karn of Mobile Suit Zeta Gundam and Mobile Suit Gundam ZZ is a scarily competent Mobile Suit pilot and ruthless dictator who almost invariably wears black, though her Qubeley is white (the colour of death in East Asia).
X-Men adversary Selene plays this dead straight. Longtime X-Man Storm? Not so much.
Rocky Horror Picture Show: Magenta wears a black French Maid uniform and a slightly more revealing black outfit throughout the film. At least, until the end when she and Riff Raff reveal themselves as aliens.
Played with in Violent City: Vanessa has been a Femme FataleWoman in White for the whole movie, manipulating her lover while retaining a facade of innocence. At the very end, once she gets to a position where she no longer needs to work through the men, she changes to all-black.
Matsu from the Joshuu Sasori series fits this to a tee, as an antiheroine out for revenge for her rape and humiliation in a Badass Longcoat done up to the neck, a Nice Hat and gloves, with only her face showing. The refusal of sexuality in particular is pretty unusual for 1972 Japan.
''Dragaera'" has Sethra Lavode; hundreds of thousands of years old, a vampire, brilliant strategist, and sorceress powerful enough to worry gods. Naturally, she lives in a mountain made of black stone, has black eyes and hair, and dresses head to toe in black. Bonus points: in Dragaera, the color black represents sorcery and is one of the House colors for both Great Houses with which Sethra is associated.
And one of her hobbies is finding new ways to use black in interior decoration.
Discworld averts the heck out of this one. Whether it's the witches or Susan Sto Helit, the Disc's women in black seem to be good. But not nice.
Additionally, Nanny Ogg has pointed out that a black dress could signify anything: "Madam or Mother Superior, it was just a matter of details."
Agnes Nitt is another variation- she starts wearing black when she's having a Gothic phase to fit in with the cool girls in Lancre, but she carries on wearing it, probably because she suffers from Weight Woe and hopes it makes her look thinner, or if not then less visible. (Of course, she's destined to be a witch anyway.)
In Doctor Who, when RiverSong returns in "The Time of Angels", she's got a lovely long black dress on that makes her look like a noir Femme Fatale. Considering it's hinted at that she served time in prison, has a secret she isn't telling the Doctor, and vandalized a home box with the message "Hello, sweetie" written in Old High Gallifreyan just to get the Doctor's attention, this probably fits. She may even possibly be the person who kills him, if the hints dropped at the end of the episode Flesh and Stone turn out to be as meaningful as they seem. So, it's safe to say this is intentional.
Contrast this with River's previous appearance dressed all in white, where she's an unambiguously good character, and her later appearance in the series five finale, where she again wears white and is very definitely on the Doctor's side.
And then her appearance in season six's mid-season finale, where some of her past is revealed — and this time, she's in grey.
Although Aeryn from the same show also liked wearing black a lot (a black leather jacket and black leather pants, to be specific), and was an unambiguously good character. It's probably some remnant of her Peacekeeper training.
When Sarah goes undercover with Volkoff in Season 4 of Chuck, she not only wears black clothing, but also has black hair rather than her normal blonde.
Nikita from the CW show Nikita had naturally black/dark hair and loves wearing black clothing. However, she is a deconstruction of this trope in some ways as she is the hero of the show as well as a complete Badass and Femme Fatale. Many other characters who were and are a part of Division favor this trope as well - in particular, Michael.
Having embraced the Dark Side completely, Morgana in Merlin is now dressed from head to toe in black.
In The Twilight Zone's episode "Spur of the Moment," a young girl out horseriding is menaced by a strange woman in black, who chases her back to her family's house. It turns out the woman is an older version of herself, who was trying to prevent her from eloping with the man who would drive her family to destitution.
The season one finale of Grimm is actually titled "The Woman in Black". The never-before-seen woman in question is seen skulking around town and kicking butt in little vignettes throughout the episode, until she turns up at Nick's house near the end of the episode and reveals herself to be his mother, who is also a Grimm and was believed to have died in a car crash several years ago. By the time she supposedly leaves town at the conclusion of the three-part episode, it's still unclear whether she exemplifies this trope or subverts it.