Rapper MF DOOM, whose persona is that of, well, a twisted genius bent on revenge against the industry that destroyed him. Possibly inspired by his real name Daniel Dumile, which is pronounced "Doom-i-lay".
In fact, the naming of someone as Hunter is apparently so iconic that some "tests" to determine the Mary Sue-ness of characters specifically have a point (or more!) for someone named Hunter. Jäger (German "hunter") likely counts.
Anime and Manga
Subverted in the Star Trek: The Original Series episode "The Squire of Gothos", with the meteorologist Karl Jaegar. Upon hearing his name, Trelane (a fanboy of Human military history) promptly squees: "Ein Deutsch Soldat, nein?"
Hunter Hearst Helmsley, a.k.a. Triple H, from WWE. Ironically, the name is a leftover from a previous gimmick as a snobby aristocrat, and was not originally given to the sledgehammer-wielding, water-spitting, all-ass-kicking-all-the-time badass we know today.
'Jaeger' is also a certain ominous bird - a kleptoparasite that beats up other birds and steals their food.
Death (or "Deth")
A favored name component of villains and Evil Overlords, although such a name is usually not given to a character at birth, but acquired later once they've reached a certain level of "badassitude".
Anime and Manga
Cancer Deathmask from Saint Seiya. The fact that his Zodiac Sign (Cancer) is also the name of a dreaded disease doesn't make him any more approachable.
Sayonara, Zetsubou-Sensei gives us the eponymous teacher's older brother, Itoshiki Mikoto - better known as Zetsumei-sensei, or Dr. Death.
Sekirei has Shiina who's name means "Death" for a very good reason despite his very sweet nature.
DC villain Deathstroke: The Most Bad Ass Name of All Time? As if that weren't enough, his full name is "Deathstroke The Terminator". His real name, Slade Wilson, isn't bad either, due to its similarity with the hard mineral slate.
Judge Dredd: Sidney De'ath became known as Judge Death before he became an undead monstrosity.
Arnold Toht from Raiders of the Lost Ark. Toht is an Anglicized spelling for the German word for "dead" ("tot").
Todd, which sounds very much like German for "death", is a common name among badasses and horror characters (though in the latter, it's because they die).
It is the middle name of detective Lord Peter Wimsey, although in his case it is pronounced "Deeth" (rhymes with "teeth"). The Wimsey books also include a psychotic neurologist named Sir Julian Freke.
The Discworld novels, despite featuring Death Himself as a prominent good guy, had a villain named Edward d'Eath (no relation) in Men at Arms.
Arawn-Death-Lord of Annuvin, from the Prydain Chronicles. Apparently Death-Lord itself is a title, as he usurped it from a previous Death-Lord (who wants it back).
Death Eaters in Harry Potter. To a lesser extent Voldemort himself (though his name is basically misspelled French for Fly From Death or Lord "I'm terrified of dying" basically).
Parodied in That Mitchell and Webb Look with Professor Death, a man who attracts military attention due to his invention of the Giant Death Ray - which turns out to be the world's first laser bar code reader.
And these are just the more notable organizations or groups with 'death' in their names. There are tons of less known ones like Death Mongers, Death Knights, Death Spectres and so on. Warhammer 40K also has weapons (like Deathstrike Missile, Deathspinner or Deathwind Missile Launcher), vehicles (Death Wheel or Deathstrike Missile Launcher for aforementioned Deathstrike Missile), occupations (Death Jester or Death Cult Assassin), ships (Agonising Death) and locales (Hive Death Mire (conveniently located on planet Armageddon near the River Insane) who fit this trope. And the multitude of Deathworlds in the Imperium.
Death Heim: the location of the final battle with Tanzra and his minions in Act Raiser.
Dracula's right hand man "Death" in the Castlevania series; like the Discworld example he is the actual Grim Reaper but unlike that example he is definitely evil.
An episode of the cartoon Mad Jack The Pirate featured a well-suited man called "Mr. D'eath". Jack remarks that his name sounds French until seeing the man upon which he realises the man is, in fact, Death.
Metalocalypse: Dethklok is all about this. Nathan Explosion, William Murderface, and Toki Wartooth all fit (and those are their birth names). Everyone that attends a Dethklok concert is required to sign a pain waiver.
Exception — De'Ath (not pronounced like you'd expect) was apparently a real English aristocratic name. Inspired Terry Pratchett for Edward d'Eath.
The Totenkopf—German for dead man's head, or Death's head—is used as an insignia for many military units worldwide. Historically, it is probably most commonly associated with the German military. It's most notorious use, of corse, was the unit which takes its name from the symbol, the SS-Totenkopfverbände: The "Death's-Head Units" of the Schutzstaffel which was responsible for administrating Nazi death camps.
The Death Cap, Amanita phalloides, which contains the same deadly poison as the Destroying Angel, and is said to have caused more deaths than any other mushroom species.
Payne in J.R. Ward's Black Dagger Brotherhood series is Vishous' fraternal twin sister. She's a warrior and shares her brother's resentment for their mother.
Doom: Pain Elemental — like the manual says: "What a name. And what a guy."
Inverted with Winston Payne from the Ace Attorney series, whose name is a play on "winced in pain". But he is actually the least intimidating adversary of the series: He's the one who's usually wincing.
Odd real-life example: One of John Wilkes Booth's henchmen, Lewis Powell — a slow-witted, borderline Ax Crazy brute who had been assigned with killing the Secretary of State — traveled under the alias "Lewis Paine".
Honourable mention must go to the commander of the Bounty, who is exactly one crossed t short of this name, and would have (allegedly) more than lived up to it.
For far less intimidating versions, Captain Planet's hottievillain Dr. Babs Blight (whose good sister is a member of the fluffy and safe naming trope, having been named Bambi).
Batman Beyond: 'And behold, I shall be a Blight upon the land, and all I touch, shall wither and die!'
When a woman has this name, the chances of four things increase incrementally. One, she's Asian. Two, she's gorgeous. Three, she is an excellent fighter. Four, any combination of those three. When a man has that name, on the other hand, we really don't know what to think.
Comic Books
DC Comics has two Jades, but only one qualifies: Jade Nguyen.
Jackie Chan Adventures. She was too young to be "gorgeous" and that also meant her usefulness in a fight was debatable, though she was shown to be able to take down anyone her own size, and occasionally larger foes.
Her adult form from the future, however, is quite gorgeous.
Jezebel Jade from the original Jonny Quest. Beautiful, tough and smart, wouldn't charge her friends for favors...too much.
One major villain in The DC Universe is named Vandal Savage. His daughter, named Scandal, is an angel compared to him, and she's still a ruthless Ax Crazy mercenary.
Speaking of Savage, Star Wars: The Clone Wars Season 3 will introduce a character named Savage Oppress, who happens to be Darth Maul's brother. Oh Crap...
Adam Savage from MythBusters, on the other hand, is someone to run with. Chances are, he's either running away from something about to blow up, or towards something he just blew up (in which case you get to see cool wreckage).
The name of the best halberd, possibly the best weapon in the game of Baldur's Gate II: Throne of Bhaal, as well as a fairly nasty demon you fight at one point.
The name of planet-life-force-eating Dark Lord Darth Nihilus' flagship in Knights of the Old Republic. There also a mentor-turned-evil with the first name Saul, as in the Old-Testament King; see "Conquerors", above. (Incidentally, Saul met his doom at a place called Endor.)
The main villain of Mazinger Z was Doctor Hell. Somehow neither that, the Evil Laughor the creepy purple skin were enough for people to figure out he was evil until it was too late.
In Shin Mazinger, on the other hand, everyone was able to figure him out rather quickly, even before the purple skin.
Integra Hellsing, though running won't help, as she's a perfect shot.
The primary antagonist of InuYasha, Naraku. The name refers to a Buddhist version of hell ("naraka").
Beyond the Grave from Gungrave, who is an unstoppable zombie killing machine. The instruction booklet of the original game also says Grave is often called "Death" by his enemies.
League of Legends has, for a while now, Malcolm Graves. He's a shotgun-toting conman who was betrayed by a fellow conman who he'd made an arrangement with. One of his skills in the game is to fire a cone of three large bullets... but his gun only has two, straight, barrels... This troper has heard the crazy awesome, if impossible, explanation that he spits the third bullet from his mouth without anyone noticing Doesn't explain why the skill is cone-shaped, but eh. Not the gunman you want to meet in a dark alleyway, that's for sure.
Harry Potter: the centaur Bane, like most of the rest of his herd, sees no reason to show humans any mercy.
There's also Darth Bane from Star Wars. Not only was he a Sith, but he tricked the leader of the Sith into wiping out the rest of the order, including himself (that is to say, the leader of the Sith).
Bane from the Forgotten Realms setting and 4th edition of Dungeons & Dragons, the god of war, conquest and fear.
Warhammer 40000: The Baneblade. Also, in the video game Dawn of War 2, there is a whole mission in which you have to actually run away from one of those monsters.
Parodied with Mr. Furious in Mystery Men, who tries to give his secret identity as Phoenix Dark, among other variations. It doesn't work, and he finally concedes that his real name is Roy.
In Tales Of The Abyss, Tear is also the name of one of the party members. It's actually short for Mystearica in this case, and she is set up as a rather morally ambiguous figure right at the start. This is subverted once you finally find out why she wanted to kill her brother in the first place.
For a double example of this, you've got the villain called KAOS (yes, all caps) in Donkey Kong Country 3 (and Donkey Kong Land 3). K name, and Chaos. And the level it's first found in is called 'KAOS Karnage', which has got to be a name to run from even faster.
BLOOD Plus Corpse Corps, anyone? Although by the time you get to the end, you'd run away from the Chevaliers.
Subverted in Darker than Black: "Havoc" is definitely a run away name, but she's actually The Atoner. It fit before her depower, though.
Eureka Seven: As if Anemone's mecha didn't already cue you in with it's black paint job, lots and lots of eyes, and frantic, slasher movie-esque theme song that it's something you should stay far, far away from, there's the fact that it's named the END.
Anemone herself could also count, as anemones are linked to bloodshed in Greek and Christian mythology.
Atrocitus, perhaps the only Green Lantern villain who can give Sinestro a run for his money in the evil name department. It's appropriate, since he's a space demon.
In the Pony POV Series, this seems to be the natural naming scheme for the Draconequi. The ones named thus far were Discord, Strife, Pandemonium, Destruction (also goes by Disaster), AnarchyEntropy, and Havoc. However, Discord and Destruction are the only ones who are actively destructive, and of the two, Discord is the only one who is truly evil.
General Woundwort from Watership Down; it's a plant (virtually all rabbits in the book are named after plants), but it contains "wound". Also, "General" as a title.
Fear Street, with the nearby Fear Forest and Fear Lake. All of which are named after the Fear family. Plus the town is called Shadyside, which is at least gloomy by itself.
Invoked in Artemis Fowl by LEP Officer Trouble Kelp, who chose his first name during his coming-of-age ceremony.
The Enemy in the Doctor Who quasi-spinoff Faction Paradox, so-called because giving it a real name would only make you underestimate the sheer scope of its power. Also arguably something there's no point running from unless you have a handy universe stored away.
Oh, and the Homeworld. Compassion too, come to think of it, and Antipathy, and... just about all the timeships, really. Then there's the Grandfather. Faction Paradox likes to do this a lot, is what we're saying.
The Harry Potter series has Dolores Umbridge as a double whammy. "Dolores" means "pain" in Spanish, and "Umbridge" is a play on the English word "umbrage," meaning "offense."
Is a guy named Karkas going to be anything but a villain?
Soulless superhuman Omega from the third Maximum Ride book.
Mediochre Q Seth has an Arch-Enemy named Maelstrom, which as a word refers to a particularly violent storm, a whirlpool or a scene of chaotic upheaval. Come to think of it, Mediochre's BadassTrigger HappyLancer is named Joseph Carrion. As in "dead meat". The Mediochreverse short story Born to Raise the Sons of Earth features a necromancer named Stormhold Elect, too.
Skulduggery Pleasent: Let's see: Mevolent, Darquesse, China Sorrows, Jaron Gallow, Murder Rose, Argeddion...need we continue?
Doctor Who has Omega, whose name is the last letter in the Greek alphabet, thus implying "the end". The trope is also parodied in the episode Closing Time when Stormageddon, Dark Lord of All is the name a three month old baby wants people to call him by. His actual name is Alfie.
Assuming you're a Dalek or other villain, there's the Doctor himself, under the alias/title "The Oncoming Storm."
Kamen Rider Ryuki: Kamen Rider Ouja's fusion Advent Beast, Genocider. It's name comes from Genocide, as in wiping out a race or species. And it's every bit as dangerous as its name implies it to be, it has a BLACK HOLE IN ITS CHEST!
The last boss in Smash Bros Brawl would be mentioned, but his name is a rather... taboo.
The Nightmare, from Metroid. An extremely creepy-looking cyborg monster that can manipulate gravity and shoot lasers all over the place, and if you blow its faceplate off (which looks bad enough on its own), its actual face is just... eurgh. The Psycho Strings that play in its theme song in Other M do not help matters.
Juggernauts (described in a terminal as "the big floaty thing that kicks our asses") in Marathon. Also, the Juggernaut Powered Armor soldiers in the Modern Warfare series.
Queen Cadavra from Bug!, a fat, evil, obnoxious black widow spider queen.
In which case, there's the real-life Mick Jagger — a bad-ass rocker if ever there was one. (The Rolling Stones, in their early days, made a point of not being nice guys like The Beatles.)
Nick Cave, as well as a few of his bandmates: Conway Savage, Roland Wolf, Hugo Race, Tracy Pew. Their music is quite often very scary.
Any of several warships bearing the name HMS Terror, but especially this one.
There was an Austrialian association footballer (soccer player) in the early 20th century whose surname was Conquest, but that's not the end of it. His first name? Norman. Norman Conquest...he was named after a bloody period of history.
There is is a Zimbabwean footballer (soccer player) called Danger Fourpence.
