Discussed in Reservoir Dogs. Joe assigns the robbers their color-coded aliases himself. When they ask why they don't get to choose, he explains that he tried that before but it didn't work, because most of the guys were arguing over who got to be "Mr. Black".
Most of The Wolfman (2010) takes place in sleepy little English hamlet of Blackmoor, that's not ominous at all!
Sirius Black, although this turns out to be somewhat misleading. It definitely applies to most of the rest of his family, though. His family attempts to deliberately invoke this trope with astronomical names multiple times. Sirius, Andromeda, Regulus, Draco, probably several of the others do this also, but I don't know astronomy well enough to tell you for sure.
To be honest, almost every character or even the spells fit into Meaningful Name: for example, Malfoy is quite similar in pronounciation (when you delve into latin languages) to "the one who was bad" - more specifically, the "was bad" part.
The Laundry Series is home to the Black Chamber, the rather...morally unsound US paranormal agency.
In The Simpsons episode "Bart Gets An Elephant", Stampy the elephant is nearly sold by Homer to an ivory dealer (and onetime whale hunter, seal clubber, and president of the FOX network) named Mr. Blackheart.
In "Kamp Krusty", there's Mr. Black, the evil camp councilor who torments Bart, Lisa, and the rest of the kids attending the eponymous camp.
The All Blacks, New Zealand's national rugby union team. They are currently ranked #1 in the world and are the World Cup champions. The name came from a typo; one writer called them "the all backs", meaning they all play fast, running games typical of the backs, but it was misprinted and the name stuck. Black is now the country's national colour, with many other sports teams being named "X Blacks" or "Black Xs".
Bubonic plague, also known as the Black Death.
Edward "Blackbeard" Teach.
Or any variation. Crimson and Scarlet sound especially Bad Ass. Vermillion, less so, but you can work with it. See also Red Baron.
Anime and Manga
For Highschool Dx D, there is the Crimson-Haired Princess of Ruin. We know her best as Rias Gremory.
The Red Comet. Also the Crimson Lightning, but he often gets confused with the other guy.
Rezo the Red Priest of Slayers has a piece of the Dark Lord of his world sealed in his eyes, making him steadily more evil through his life. Lampshaded by Lina when she comments that his name sounds like a villain's after they meet and he tries to play her into giving up a powerful artifact.
Erza Scarlet is one of the few character who can discipline Natsu.
Now we also have Mavis Vermillion, Fairy Tail's first master, who might be joining Makarov and Gildarts as the Big Good.
Solf J. Kimblee the Crimson Alchemist could also be considered this especially considering What he did in the War of extermination in Ishval
The Red King, Suoh Mikoto of K also qualifies. While he's usually pretty laid back and downright lazy, once he gets down to business there is no stopping him. He is more than once described as violent and a berserker, blows up whole buildings and takes down an elite team without even blinking. Just ask Awashima how dangerous he is.
While not a person's name, the Scarlet Crusade from World of Warcraft. Originally devoted to slay undead, but turned into an army of insane religious zealots bent on killing anyone who's not one of them. Also, their leader is a demon/vampire in disguise.
Subverted in Final Fantasy VII: Scarlet of Shinra is utterly laughable as a villainess, present only to fill the role of The Vamp. All she manages to do is be annoying enough that you can't help but relish the literal bitch-slap fight atop the Sister Ray.
A very bad example is Scarlet Foxfire, which has a color, animal, and fire, from the webcomics of David Gonterman. Gonterman probably does actually intend her to be a badass, but seeing as how she's some sort of superpowered vixen fursuit (worn by a guy), well, her status is dubious, at best.
The Victorians and Edwardians loved to associate this with madness and decay as the symbol of the plague is a yellow flag with a single black spot flown above an infected vessel or building. In other cases, it might just be related to inherent abilities of lightning and/or awesome reflexes. If the word "gold" is used instead, it may simply be a reference to wealth and/or greed.
Anime and Manga
Minato Namikaze A.K.A. the Yellow Flash. The ONLY Ninja listed in the Black Book with a "Run On Sight" tag...
...Not that it would help much if he was after you.
The manga of Cowboy Bebop featured a reporter following the crew as they chased the White Siblings, Ash and Blanche, who preyed on the elderly.
The White Devil, Nanoha Takamachi. Well, it's a name to run from if you have done anything to incur her wrath. Okay, so she won't cause any lasting damage, but you are going to be in one hell of a lot of pain...
White Devil already spread fear fsince 1979 as the nickname Zeon forces gave to the RX-78-2 Gundam and his pilot Amuro Rei.
Albert "Chalky" White, from Boardwalk Empire is either a Villain Protagonist or an Anti-Hero, but he's most definitely someone you do not want to cross. Extra irony points for Chalky being a black man with three names meaning "white".
Lucien Lacroix from Forever Knight...granted, his original Roman name was 'Lucius', but he still gets points for being a villain with a name that means 'white' or 'light'.
Pink doesn't seem scary until you remember that in Power Rangers Lost Galaxy it was the Pink Psycho Ranger that was not only the last to be killed, but also caused the death of the first ranger in Western Power Rangers history. Seven seasons in, and it was an elite mook that was pink nonetheless, that finally killed one off.
In Russia, more hardcore communists sometimes call those whom they deem communists in name only "white-pinkies" (belo-rozovy), combining the former use of "pinko" with white, the color of anticommunism since the Civil War.
Clear World and Clear Vice Dragon in the Yu-Gi-Oh! card game are clearly dangerous. The first inflicts a harsh penalty on each player for each Attribute of monster they have on the field, while the second renders its controller immune to the penalties of the first and attacks with twice the attack power of whatever it's attacking.
In the Touhou series colors can be associated with power. The color purple usually represents power. It stands to reason that the most powerful being/Youkai in Gensokyo, Yukari Yakumo's name is Japanese for Purple. Also her shikigamis, Ran and Chen, have names that mean Indigo and Orange, respectively.