"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, Kal-El etc.) Except when they're not (Azrael and any angel from Shin Megami Tensei for example)
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" note Likely because it means "spotted". Yes, the lord of the underworld named his dog Spot, and became the Ur Example of "Spot" as a dog's name..
Apocalypse from the X-Men is also referred to as "En Sabah Nur". That's 30th century BC Egyptian for "Kick Your Ass."
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 same author, there's the Codex Alera series, which has every name derived from Latin. The absolute crowner, however, has to be Gaius Tavarus Magnus, which translates into Lord Wolverine The Great. He's not a bad guy, but he certainly earns it.
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").
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.
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.