Names to Run Away From Really Fast which inspire fear because they are fearsome adjectives: Vicious, Grim, Sinister, Nefarious, Horrible, etc.
Or they inspire mistrust because they sound "false", like "honest".
Yami (= Dark) Yugi, whose early punishments for people who attacked or threatened his friends included tricking people into yoyoing themselves through a roof to fall several stories, getting people stung by their own scorpions and subjecting people to illusory torture by Eldritch Abomination.
A common misconception surrounding Star Wars is that Darth is Dutch or German for dark, when neither of these statements are accurate. Dark would be donker and dunkel, respectively. Vader, on the other hand is Dutch for father, though it is pronounced differently in Dutch.
Pokémon Colosseum: It may be an unwritten rule that the leaders of Cipher have some part of Evil in their name. First was Evice, and second was Greevil. For added evil points, Greevil's Japanese name translates into 'Deathgold'.
Darth Sidious of Star Wars. Double points for rhyming with "hideous". There is a certain in-story justification, as Sith 'names' are not technically names, but titles given after they've purposely started down the road of evil.
Colm Meaney, an Irish actor who is actually by many accounts a pretty nice guy. Doesn't help that outside of Star Trek fandoms he's mostly known for playing villains or at the very least hard-assed Anti-Hero types.
Adam Savage from MythBusters: His job involves smashing, blowing up, or otherwise destroying various items in big and spectacular ways (and he is very enthusiastic about his work). Also, in episodes where the crew play out character roles, Adam often plays villainous characters with "Savage" somewhere in their name (i.e. Baron von Savage, Captain Redbeard the Savage).
Vishous from J.R. Ward's Black Dagger Brotherhood novels, mercifully shortened to 'V'. Most of her male characters have bizarrely spelled "badass" names, including Torhment, Phury, Zsadist, Rhage, Rehvenge, and Wrath (well, that last one is spelled correctly). John Matthew doesn't fare any better with his warrior name: Tehrror; as does Butch when he's revealed to be a half-breed and gets saddled with a vampiric name of legend: The Dehstroyer.
Venandekatra the Vile in Belisarius Series. It is specifically noted that other names(like "Grim") carry a compliment with them as well as an insult; they imply that someone is a Magnificent Bastard. Whereas vile is just an insult.
Subtly, several names translate to disabilities, though that's not always bad. On the good side, Cecile from Code Geass ("Blind"). On the bad side, Claudia from The Vampire Chronicles ("Lame"). "Cecile" comes from "caecus", which means "blind" in Latin. In olden times it implied powers of prophesy as well, since many famous seers (Tiresias for example) were blind.
Idlebury from Be Careful what you wish for by Stef. Its citizens are constantly idle (i. e. lazy).
Skulduggery Pleasant: Ghastly Bespoke, Baron Vengeous, Mevolent, Auron Tenebrae, Gruesome Krav, Christophe Nocturnal...the list goes on. Justified as they chose the names themselves.
How to Train Your Dragon is full of this: Grabbit The Grim, Gormless The Grim, Stoick The Vast, Grimbeard The Ghastly, Norbert The Nutjob, Madguts The Murderous, Murderous The Magnificent, The Seadragons Furious and Merciless, and, of course, Alvin The Treacherous.
Spoiler from The Key To Rondo. The kids quickly realize he's bad news, and suspect that he's working for the Blue Queen. Worse, he's actually Leo's Wicked Uncle George, who had given the eponymous Key to the Blue Queen so she could run the world while he lived in luxury.