A form of Names to Run Away From Really Fast: Since "mors" is Latin for "death", and many Latin-derived modern languages use something with a close resemblance (French "mort", Spanish "muerte", Portuguese or Italian "morte", etc, or even worse German "Mord" for "murder"), any name with mor- or mort- can be used to indicate death or evil.
Morlun from Spider-Man. This guy, among other things, ate Spider-Man's EYE. Then killed him. Sure, Peter got better, but still. Also, Morbius The Living Vampire.
In J.R.R. Tolkien's invented Elvish languages, "mor" means dark or black, hence it often appears in "evil" names: Morgoth ("Dark Enemy", Supreme Big Bad), Mordor ("Black/Dark Land" of Dark Lord Sauron), Morannon (the "Black Gates" into Mordor), Minas Morgul ("Tower of Dark Sorcery"), Moria ("dark pit"). But mor also appears perfectly innocent at other times, e.g. in the girl's name Morwen ("dark/black maid", referencing hair color).
Morlocks - From the novel The Time Machine, which was the namesake of X-Men's Morlocks and the basis for the novel Morlock Night (which makes them even more intelligent and dangerous).
And Dean Moriarty from On The Road who gets his name from the above. While not evil, he is a morally loose character who seems to come apart at the seams at the end.
Oh, and Moriarty's right-hand man, Colonel Sebastian Moran
Word Of God has it that Moriarty was named after a real, extremely violent, criminal whose name Doyle spotted in a newspaper.
Voldemort - Harry Potter, of course, meaning "Flight of death" or "Theft of death" in French. And if you say his name in Deathly Hallows, you really do have to Apparate. Really fast.
Bonus points to him for making it up himself with an anagram of his real name.
Tom Marvolo Riddle = I Am Lord Voldemort
There's also the spell which summons his Death Eaters' symbol, Morsmordre.
As well as his relative, Morfin Gaunt, who has a tendency to nail snakes to doors.
Mort, of Discworld is an exception, as despite being Death's Apprentice, he's a skinny little nervous guy...until he gets into his role...
Morkai the Red, a minor character but powerful wizard in the early Drizzt novels, who is vicious and dogged in paying back those who killed him.
Moridin from the Wheel of Time. Dangerously insane, third most powerful evil person in the world (after the Dark One and his avatar), name literally means "death" in the Fictionary of the books, and just to top it all off, his previous name: Ishamael, a.k.a. Ba'alzamon. Oh, like it wasn't obvious.
Mordeth from the same series. Bonus points for having the English word "Death" in his name as well.
Mordion from Hexwood, who has the face of a skull and is tasked with killing political enemies.
Morgra from David Clement-Davies' novel "The Sight".
The Neverending Story has the villain G'mork, the servant of the Nothing, and Morla The Ancient One, who, while not being a villain, represents the nihilism and atrophication which allows the Nothing to take hold.
Mabinogi Fantasy Life has Morgant, also known as Dark Lord, who is both The Dragon and has yet to be defeated in the mainstream storyline; both times you actually fight him the dialogue suggests he let you win, although Tarlach does manage to knock him out temporarily in a cutscene.
Subverted with Mortimer Brewster from Arsenic and Old Lace. He reviews murder plays for a living, but, unlike several other members of his family, he hasn't committed actual murders.
General Donald "Devil Rebirth" Morden from the Metal Slug games.
Gym Leader Morty subverts this. His name alludes to the fact that he uses ghost types - but he's a really nice and easygoing guy.
Albeit a bit cocky. *
"It's said that a rainbow-hued Pokémon will come down to appear before a truly powerful Trainer. I believed that tale, so I have secretly trained here all my life. As a result, I can now see what others cannot. I see a shadow of the person who will make the Pokémon appear. I believe that person is me!"
Mordin Solus from Mass Effect 2. Sure, he may be a scientist primarily, but he's also a highly trained and extremely efficient killer, and he's not afraid to tell you so.
Do not sleep with Morinth. Should you chose to ignore this warning, you should make sure your life insurance and will are up to date.
Mortimer McMire from the Commander Keen series, who has tried to destroy the Earth (Invasion of the Vorticons), the galaxy (Goodbye Galaxy), and even the entire universe (if the Universe is Toast trilogy had been made, that is...)
Mort the undertaker in The Curse Of Monkey Island — though he's a Harmless Villain (if that) with exploitable superstition. He eventually helps you once Murray threatens to curse him with the inability to "find socks that match."
The initial villain in Tales Of Vesperia is called Mordio. However, this is subverted when it turns out that "Mordio" is an imposter and the real Mordio is one of your party members.
