Kane from Beyblade, at first glance, seemed to be an aversion to this trope, being a sociable and helpful team leader who easily befriends Takao. Then he goes Brainwashed and Crazy...
Cain of Count Cain/Godchild. While he's actually the protagonist, he was given the name because his father believes him to be cursed. He has a troubled past, is known as a ladies' man, collects poisons for a hobby, and has the unlucky tendency of having the people around him die often, and in gruesome ways.
However on his death, Alexis reveals that he named his son "Cain" because even though the biblical Cain committed a terrible sin, God still forgave and protected him, and eventually allowed him to settle down.
Golden Cain. The title refers to the main character's enigmatic love interest who's trouble, to say the least.
Teknoman, the US adaptation of Tekkaman Blade, renames Evil Twin Shinya Aiba into Cain Carter... possibly to make up for renaming his tekkaman form to Teknoman Saber instead of the extremely descriptive "Tekkaman Evil".
The name Cain actually makes sense here, though: Based on the flashbacks, it seems that the twins' incredibly screwed up parents had been intentionally goading their sibling rivalry into full blown homicidal malice for pretty much their entire childhood, before anyone had ever heard of a tekkaman.
The Trigun anime used a guy named Kaine the Longshot to replace a less family-friendly villain in the manga version.
Sergeant Cain Fuery of Fullmetal Alchemist. Subverted in that he's a rather shy and somewhat geeky communications officer.
Word of God says that the author picked most of the first names for more minor characters at random from a dictionary of European names.
It's actually a misromanization of Huey, after the iconic helicopter, as part of the military characters' Theme Naming, all of them being christened after military aircraft. Huey Kane does sound a bit more fitting for the character.
Prince Cain from Reimei No Arcana. He is Caesar's older half-brother and the first-in-line to the Belquat throne. However, he holds a strong hatred for Caesar as Caesar's mother was put as queen while Cain's mother was dethroned, Caesar has black hair (hair color is taken as Serious Business with black hair being the most favorable while the rest of the hair colors are seen as "common"), and Cain's fiancee Louise has feelings for Caesar.
A combined subversion and straight use of the trope in GaoGaiGar: The Cain of this series is Leader of an alien civilization destroyed by the Zonder. Cain also developed the G-Stone technology and sent Galeon to Earth with his son, Latio (AKA Mamoru). In short, a strong candidate for the show's Big Good. However, in FINAL, A replicant of Cain, named Pei La Cain, acts as one of the villainous 11 Sol Masters. Notably, his only two contributions to FINAL's plot are a brief appearance that costs Guy dearly in his first duel with Palparepa, and serving as Mamoru's opponent in the final battle.
Kathy Kane, the original Batwoman, and her niece Bette Kane, Bat-Girl. Unambiguously heroic, but usually treated as pests or second-raters by Batman, whose mother's maiden name also happened to be Kane. Probably named after Batman creator Bob Kane, who appears not to have been a real-life example of this trope. Maybe. The current Post-Crisis Batwoman, Katherine "Kate" Kane, has been drawn into the inner workings of the Religion of Crime due to her presence at the heart of their prophecies regarding the "twice-named Daughter of Cain". As a "twice-named" (referring to her twin sister, who she thought was lost as a child) and the daughter of a "Kane," the religion has become somewhat preoccupied with her sacrifice.
Cassandra Cain, the second Batgirl, is usually heroic, but has some trauma to her backstory. Her father, David Cain, was an assassin. (Her name is probably a Mythology Gag for the first Bat-Girl.)
Kaine from the Spider-man Clone Saga. Being an unstable, overpowered psycho clone who simultaneously loves and hates Peter Parker (and Ben Reilly) is pretty fitting here. Anyone he killed had an ugly scar on his face called "The Mark of Kaine" (and he could even put this mark on someone without killing him if he wanted to make a serious point.
Cain was the sinister trickster host of DC's horror anthology series House of Mystery; his brother Abel hosted its sister series, House of Secrets. While originally the names weren't strictly meant to say that they're theCain and Abel, their appearances as supporting characters in The Sandman established that they were really a pair of Starfish Aliens from billions of years ago who were the first sentient lifeforms in the universe to intentionally kill another of its own kind and its victim. The first act of murder was so monumental that they became archetypes living on for all of history in the collective unconscious of all life, perceived by each new observer as one of their own and inspiring stories such as the Bible story of Cain and Abel. It's interesting to note that while Eve is also a character in the comics, she does not consider herself to be related to them and denies it when Cain calls her "Mother". Cain responds that she is "everyone's mother", and leaves it at that.
Joshua Kane, hunter of big game and werewolves in Werewolf by Night issue 4 and his unscrupulous businessman brother, Luther Kane.
Alien: Kane was the crewmember who "gives birth" to the terrifying xenomorph.
May be averted as the crewmember Kane is not a bad guy, just a terribly unlucky guy who found himself at the wrong place at the wrong time.
Averted in Lifeforce. Special Air Service Colonel Colin Caine is completely heroic.
In Hollow Man, Dr. Sebastian Caine becomes invisible, and gradually goes mad with the power it gives him.
In the The Haunting (1999) spoof in Scary Movie 2, the villainous ghost was called Hugh Kane. The original character in Haunting was called Hugh Crain, technically getting just around this trope even though it's still evoking the phonetic symbology of the trope.
Early drafts of the script for what became A New Hope had Luke Skywalker called Annakin Starkiller, the son of a well-known warrior named Kane.
In Pat Conroy's novel The Lords of Discipline there is an antagonistic character named Cain Gilbreath. Lampshaded mercilessly by the main character.
The Jeffrey Archer book Kane and Abel, although Abel wasn't portrayed as the "good" one.
Solomon Kane, Robert E. Howard's swashbuckling Puritan hero.
Karl Edward Wagner's Kane, who is in fact a Conan-esque (that's the description for those who have never read the Kane books... he's actually not much like Conan at all) version of the Biblical Cain, with stories that take place in a dangerous and dark prehistory. Kane himself was cursed with immortality by an insane elder god after having strangled his brother, Abel.
From the evidence given in the stories, it's pretty clear that the insane elder god is meant to be Jahweh, ie: God
From The Bourne Series, Jason Bourne's codename in the books is Cain, and after Bourne's brother is brutally killed and Bourne is framed, one of the characters wonders if the name hadn't been prophetic. Also, in the movies, an alias of his is John Michael Kane.
Caine of Garthan Hold (aka Hari Khapur Michaelson), of Matthew Stover's The Acts of Caine, who definitely has the morally ambiguous Bad Ass anti-hero thing down pat.
Ciaphas CainHERO OF THE IMPERIUM!!!, a Fake Ultimate Hero, has not one but two names with unfortunate Biblical implications. He doesn't have any siblings, though.
The Ellery Queen novel "The King is Dead" features rich munitions maker King Bendigo, his wimpy brother Abel, and his drunk brother Judah. King Bendigo's real first name is Cain. He's the Big Bad even if he is not the murder but the victim.
The Caine in The Caine Mutiny. Tom Keefer even specifically says he feels the ship, a WWI relic held together by rust and grime, is as detestable as its Biblical namesake.
Valkyrie Cain in Skulduggery Pleasant is one of the good guys, but she specifically picked her name based on the expression 'raising Cain' (making trouble).
Subverted by Robin Kane, who is a teen girl detective, sort of like Nancy Drew.
Admiral Helena Cain in Battlestar Galactica (Reimagined), commander of the Battlestar Pegasus. She quickly turns out to be a fanatical General Ripper so consumed with the war against the Cylons that she commits atrocities against civilian fleets.
Wyatt Cain from the Sci Fi Channel's Tin Man, and the Tin Man in question. All around Badass Normal, ex cop and ready for vengeance. But only against the people who destroyed his life and killed his wife and son (he believes).
Duncan Kane (and his morally dubious dad Jake Kane) from Veronica Mars.
When Stavros Cassadine came back to life on General Hospital, he sometimes used the alias Lucien Caine, and even fantasized about calling his hated brother Stefan's attention to the Cain/Abel echoes.
The Band's "The Night They Drove Old Dixie Down" begins with the line "Virgil Cain is my name" and includes a line reference to raising a Cain back up.
Completely averted by Paul Simon who used the pseudonym "Paul Kane" for some of his early compositions. At the time he was more concerned about the anti-Semitism he might experience from using his Jewish surname than the negative Biblical undertones of his pseudonym.
Kane of WWE. His backstory is that the seven foot tall monster was burned as a child and raised by "manager" Paul Bearer. He is also brother to The Undertaker; although both are dark and evil characters, the biblical brother theme is still present. And then there's the whole "sadistic pyromaniac" aspect of his character, which makes him seem even more demonic. He has since suffered some character decay, according to some.
The Undertaker actually debuted as "Cain the Undertaker", although he dropped the Cain part after a few months.
When Harlem Heat (Booker T and Stevie Ray) first arrived in WCW in 1993, they were billed, respectively, as Kole and Kane.
Warhammer 40,000 plays this one straight with Khaela Mensha Khaine, the Eldar god of war. In Warhammer, he's the God of Murder.
To the Dark Elves maybe, the High Elves still consider him to a God of War, just one that you don't turn to unless you need to.
Also subverted with Commissar Ciaphas Cain (HERO OF THE IMPERIUM!), the hero of the eponymous book series. He's a self-professed coward who gets by with a lot of luck, however, he's still plenty Bad Ass and has taken on some of the worst the galaxy has thrown at him and come out on top on most occasions.
Sera Myu has Cain the Dark who is the biblical Cain as a spirit possessing Sailor Astarte and later a homunculus made for him.
The Legacy of Kain series stars a vampire named Kain, who later goes on to conquer the world, lead it into ruin, execute plan after plan to save it... Kain's not a nice guy, but he doesn't start off evil and it's indicated that he doesn't end the series all that evil either. Still not nice, but...
Lucas Kane, protagonist of Fahrenheit, spends most of the game on the run from the cops after killing a man. Admittedly, he was possessed at the time, but still.
The Kain family from Pathologic. Though they aren't evil(there are no exact villains in the game), they are still creepy and mysterious - the recently deceased patriarch of the family was a seemingly immortal man, his sister-in-law was resident The Caligula, and her daughter is obsessed and probably in love with one of the protagonists.
Mega Man X series' Dr. Cain isn't a bad guy, but his attempts to copy Dr. Light's research has ended in disaster. (Guess Dr. Cain forgot about the whole "30 years of brainwashing—er, I mean, ethical training".)
In the NES version of Strider, one of the supporting characters is named Strider Kain. Strider Hiryu is sent to kill him because he's fallen into enemy hands (Striders caught by the enemy are considered expendable since their identities are now known), but the situation becomes more complicated than it seems.
Xenogears has an Emperor Cain. And an Abel, no less!note Although he doesn't actually succeed in killing Abel, just his girlfriend/adoptive mother who protected him via Heroic Sacrifice. Yeah. The game's filled with Biblical references, after all.
Kain R. Heinlein, also from Fatal Fury. Best friend to Abel "Grant" Cameron. You see where this is going right?
Not a character example, but the M-920 Cain is the most powerful weapon in Mass Effect 2. One shot will kill almost any enemy in the game, and the final boss can only take two hits. It has two drawbacks however: a long charge up time and a blast radius large enough to easily kill the player.
In Ultima VII, an alchemist named Caine appears as a ghost on the now-dead island of Skara Brae. He blames himself for this, as he attempted to make a substance that could kill the lich Horance who was taking over the island, but botched the mixing process which resulted in a colossal fire that destroyed the island. Subverted in that it actually wasn't his fault, but he inadvertently started Batlin on his path to darkness.
Cain in Galerians is a textbook example of this, being a jealous, villainous, and murderous brother.
Cutter Cain, who kills Seers, typically with a knife, in City of Heroes : Going Rogue; Subverted in that his actual name is Doctor Steffard; he's actually a ResistanceWarden trying to help them by removing cybernetic implants binding them to mindless slavery; but the science is so experimental it's not always successful, and at least one was killed by a remote kill-signal in the implants after he had released her.
A character named Caim (a Gaelic spelling of Cain) is the main character of Drakengard. His moral compass can be described charitably as "Anti Heroic" — in fact, the only thing that keeps him from being a Villain Protagonist is that the target of his Roaring Rampage of Revenge happens to plan to Take Over the World (and for the record, Caim would still be butchering them all even if their goal happened to be 'build the world's happiest puppy orphanage'). By the second game he's turned into an antagonistic Rogue Protagonist, who seeks to free his pact partner from the Knights even if it means she'll destroy the world when freed.
Hatoful Boyfriend has a fantasy AU in which Yuuya's name is Cain Reprobus. The fantasy AU reflects the normal canon in many ways - Cain's a paladin, a healer-fighter and Knight in Shining Armor much beloved by his people, but his name hints about how Yuuya killed one brother to save another and regrets it, and tries to atone through general heroism.
Episode 11 of Symbionic Titan has Lance and Illana escaping a mysterious prison with a fellow prisoner named Cain. He's actually a good guy...until he turns out to be The Dragon of the bad guys.
Abraham Kane of Motorcity, the show's Affably EvilBig Bad obsessed with crushing what little population of Detroit remains outside of his rule. He even has a fitting voice, being played by Mark Hamill.
Kane Hodder is an actor-slash-stuntman who is solely credited as portraying Jason Voorhees in four (consecutive) films in the franchise's history (Part VII: The New Blood, Part VIII: Jason Takes Manhattan, Jason Goes to Hell: The Final Friday, and Jason X). He also did stunts for Leatherface's actor in Texas Chainsaw Massacre III. All in all, "horror movie badass extraordinaire" probably looks good on a résumé.
Michael Caine, best known for playing Lovable Rogue type characters. It's a Line-of-Sight Name. He was originally going to change his name to Michael Scott, but that name was taken, and he happened to spot an ad for The Caine Mutiny. He has joked in interviews that had he looked the other way, he would have ended up as "Michael One Hundred and One Dalmatians".