"Smilodon fatalis narrowly edged out Tyrannosaurus rex to win this year's Most Badass Latin Names competition, after edging out Dracorex hogwartsia and Stygimoloch spinifer (meaning 'horned dragon from the river of death') in the semifinals."
Anyone/thing with "Bal-" (Baal) in their name. "El" (meaning "god") is the non-threatening version (Jor-El, etc.)
Variants on "Cain" are a twofer, being both a really old name, and a notorious murderer; in fact, the person who invented murder.
Any villain/weapon/organisation etc. called Cerberus; that has the added kick of an animal name (the three-headed dog which is said to guard the gateway to Hell to prevent anyone escaping). Strangely enough, nothing villainous ever seems to be named for the Greek original of this name, "Kerberos".
Vermithrax Pejorative, "The Thracian wyrm that makes things worse", from Dragonslayer.
What about Zuul, Vinz-Glortho, or Gozer the Gozarian? Albeit they are more like made up dead languages...but who cares when you are being told to choose the form of the Destructor?
Carcer is Latin for prison (the root of our incarcerate) and is also the name of the villainous murderer-cum-policeman in Terry Pratchett's Night Watch.
The Big Bad of Kitty Norville, being a vampire from the time of ancient Rome, has a Latin name by which he is known: Dux Bellorum, 'leader/general of wars'. 'Nuff said.
The name of Bellatrix Lestrange from Harry Potter means something akin to "Female Warrior the Crazy".
Dolores Umbridge. Dolor=pain or sorrow; umbra=shadow.
Lucius, Narcissa, and Draco Malfoy. 'Lucius' is from the same root as 'Lucifer'; 'Narcissa' is the feminine of 'Narcissus', the name of a beautiful, but poisonous flower; 'Draco' means 'Dragon'; 'Malfoy' means 'Treachery.' Considering that JKR got her degree in Classical & Romance Languages, it is not surprising that many of her character's names follow this trope.
From The Dresden Files, we have Nicodemus Archleone. Two Biblical references with one name — and he's old enough to have met Jesus. He has the experience to show for it, too.
Janos is an alternate spelling of Janus, the Roman god best known for being two-faced. It is also the name of the commander of the King's Landing city watch who betrays Ned Stark in Game Of Thrones.
Borborygmus Gog in Galaxy of Fear. Borbogrygmus is the official term for stomach sounds; it comes from an ancient Greek word.
Any vampire series; it's the ones with these names you really better watch out for. "Angelus" from Buffy the Vampire Slayer for example.
Shows up in Stargate SG-1 a whole lot. When your Big BadAlways Chaotic Evil race's shtick is stealing the names of the gods from primitive Earth religions what else would you expect? e.g. Ba'al, Chronus, Sokar, Anubis, ect.
In one episode of Doctor Who, The Master uses the alias Magister (Latin for "Master"). In another, Thascalos. (Greek for "Master").
Arcturus Mengsk. More intimidating for political reasons than physical.
Blizzard finally admitted that "Zera" means oblivion in Khalani. Admittedly a made up language, but do any Protoss heroes with that in their name come to mind? Zeratul!
In Soul Calibur, Zasalamel's (an immortal) attacks are named after Babylonian gods, sets up the events of the 3rd game for his own benefit, and while heroic in the 4th, is still a jerk.
The titular planet from Anachronox. "Poison of the past"
Vanitas. Latin for emptyness. Amusingly enough, an alternate interpretation is "futility".
Gilgamesh in Fate/stay night. Considering the fact that it revolves around a war between the summoned spirits of legendary heroes, it's not just a guy named Gilgamesh, it's theGilgamesh.
Nex; Latin for Murder, an apt name for a monster that even the gods themselves feared. It took the combined power of four armies to seal Nex and her Zarosian soldiers away, and she has broken free twice.
Mega Man Zero: Omega Zero, AKA the God of Destruction, who singlehandedly killed 50% of humanity and 75% of reploidkind during the Elf Wars. That is what Dr. Wily wanted Zero to become.
Ulysses from Lonesome Road takes the Latin name of Odysseus.
The League of Legends champion Aatrox derives his name from the Latin atrox—the same word from which English words like "atrocious" and "atrocity" are derived.
Semi-exception: Optimus Prime and Ultra Magnus are ancient by human standards, but a few million years is pretty standard for a giant alien robot, and they're nice folks. But extremely Bad Ass nonetheless.
