General Peters-Stahl, one of the few outright villains in Scrapped Princess. Also worth noting is that Cz, the only Peacemaker who is supposed to be sympathetic, is also the only one that isn't blond.
Fist of the North Star has Shin and Souther. Raoh was originally blond in the manga as well, but was given black hair in the TV anime series (the newer anime versions restores his original blond hair). This is evened out by Jagi in the original anime (whose hair color was changed from the manga's black to blond), who was not only purely evil, but also the one who turned Shin evil in the first place.
Johan Liebert of Monster is handsome, blond, blue-eyed, and absolutely terrifying.
Chrono Crusade has Joshua Christopher, a blond, blue-eyed Ill Boy who's manipulated by the White Hair, Black Heart guy into becoming one of his minions after he puts on a pair of demon horns (which also drive him absolutely insane). However, the series also has Father Remington, another blond man who may be one of the most genuinely good characters in the series.
Mello from Death Notehas been a Mafia terrorist since he was 14, armed with guns in leather pants. Plus taking extreme measures to get what he wants, including kidnapping a teen girl and causing her to go through a traumatic experience that leaves her catatonic.
A flashback story revealed that Hiruma from Eyeshield 21 has hair that is naturally black, but he dyes it specifically as part of his strategy to make himself look more intimidating. It works. Oh, and he's evil.
Every notable blond guy in the series is (or was) a jerkass, with the exception of Homer and the Yuuhi Guts captain. The biggest jerks in the Pentgram are blondes, Hiruma and Agon dyed their hair blonde at some point, and former delinquents Toganou and Juumonji started out as jerks to Sena. Somewhat justified for the Japanese characters who are blonde, since bleached hair = delinquent = jerk.
Although he's amusingly psychotic to the point where it's hard not to like him to an extent, Ladd Russo from Baccano! would most definitely fall under this trope, if not for undecidedly brown tan AND dark blond hair which turns gray for artisticness in Alcatra. I mean, come on. He shoots a small child's head off and constantly threatens to kill his girlfriend, among other things.
The whole 'kill his girlfriend' deal is very happily mutual, seeing that she's a Death Seeker; it also subverts the whole Morality Pet trope by emphasizing how totally batshit insane both of them are.
Played with in The Prince of Tennis. Kevin Smith is an angry, bitchy, aggressive American boy who is an absolute Jerk Ass for quite a while...and comes from a broken family with a negligent father, also blond. When he's defeated and comes to terms with himself, he shows a sweeter side, though not losing his strong temper completely.
Code Geass has Prince Clovis and V.V.. The former is an insecure wreck who commits mass slaughter to cover his screw ups, the latter is just plain insane. Charles di Britannia had dark blond hair (comparable to Nunnally's) before age turned his hair white. Then there's also his second son Schneizel.
Krad in D.N.Angel, who is also a prime example of Light Is Not Good thanks to his angelic appearance and utterly sadistic personality.
Cain from Trinity Blood is blond, angelic looking, and a completely evil bastard.
Fushigi Yuugi's Nakago (bonus points for being the sole survivor of his repulsive, entirely-blond tribe).
The nearest immediate subversion is Speedwagon, who came from a very similar background as Dio, and in his first appearance mugs Jonathan in a dark alley. After his defeat and Heel-Face Turn, he becomes a loyal ally and later a highly affluent philanthropist.
Brando's most loyal subordinate, Enrico Pucci, is not only this but also subverts the Dark-Skinned Blond trope by being pretty damn cunning.
By the looks of it, part 7 villain Funny Valentine is also one.
Gin from Detective Conan, although there is conflict over whether his hair is blond or silver.
Darker Than Black very much fits both this trope and Blondes are Evil, given the huge amount of blond Contractors, who, while varying in terms of morality/likability, are all superpowered sociopaths. The high proportion of blonds might be because Contractors are generally foreign agents, and the favored way to depict a white foreigner in Japan is through blond hair and blue eyesnote which incidentally once used a Darker Than Black character as the page image.
Vincent, and with heterochromia, to boot. Subverted. Vincent turns out to be not such a bad guy after all, just fiercely devoted to his older brother and rather extreme in his methods.
Jack, on the other hand, averts this trope and then plays it straight.
Hellsing has The Major, The Doctor, Luke Valentine, and Warrent Officer Schrödinger. Also Enrico Maxwell, but only in the manga. Father Alexander Anderson is a subversion. In his first appearance, Anderson seems like a straight-up villain, but he's very much an Anti-Hero and Noble Demon. And the same applies to his protégé, Heinkel.
Asuham Boone from Overman King Gainer is vengeful, believes in Revenge Before Reason, and is utterly obsessed with capturing co-protagonist Gain Bijou. If he has to endanger innocents or manipulate subordinates to do so, he will.
Justin in Soul Eater. Blond haired, blue eyed priest, no less. In hindsight, it was probably too good to be true and very easily dismissed on the basis that the series has a cast full of oddities, as it were.
The Oni Clan in Harukanaru Toki No Naka De is probably deliberately presented as evil foreigners, and anyone with blond hair is labelled as evil by the locals.* Ironically, Shimon, who also gets bashed for similar appearance, is one of the nicest members of the main cast. While this attitude is likely intended to reflect the general time-appropriate xenophobianote Haruka's world is based on Heian period Japan, the Oni do actually possess destructive powers and therefore present danger. In reality, though...Akuram is corrupted by his powers; Ikutidaru repeatedly questions their plans; much of what Shirin does is of the Love Makes You Evil kind (and she isn't even blond to begin with); Sefuru has a Freudian Excuse and isn't mature enough to comprehend the situation. Then you get into the clan's backstory...
Blassreiter: The reason Xargin is so pretty is so that you'll like it when he murders you...or turns you into a homicidal cyborg.
Vash the Stampede, aka "the Humanoid Typhoon", is also blond (though at least in the anime it's a slightly darker blond than Knives', and in the manga his hair turns progressively darker as the story advances) and believed by most people to be a walking disaster area (with, it must be conceded, some justification).
In Saint Beast, Pandora is not only a bit of a jerk but can also be considered outright evil for his complicity in so many awful things, no matter how he feels about the acts themselves.
Naruto has Deidara, who's completely insane. Naruto himself is an aversion.
Bunbee of Yes! Pretty Cure 5 had blonde hair in his human form. Interestingly, he survives the first series, shows up in the sequel Yes! Pretty Cure 5 GO!GO!... then promptly has enough of being evil and decides to pull a Heel-Face Turn in time to show up in the Pretty Cure All Stars movies.
The only physical difference between The DCU's Impulse and his Evil Twin Inertia is their hair; Impulse has brown hair, Inertia has blond.
Wilhelm Ryan, the villain from The Amory Wars/Coheed and Cambria.
Jan Arrah, Element Lad, the villain of the Legion of Super-Heroes story Legion Lost, is innocently handsome and blond. Note, he was blond for thirty years worth of stories before he was made a villain.
Kordax, the ancient Atlantean prince in Aquaman and the greatest villain in Atlantean history. His blond hair was actually seen as a sign of evil by the people of Atlantis, especially in the royal family, which is why Aquaman was abandoned at birth.
One of the more notable feuds in Marvel Comics is that between the short, dark, noble Wolverine and the tall, fair, psychopathic Sabretooth.
Neron, The DCU's lord of Hell for a time in the late '90s and early '00s, appeared as a tall, muscular, pale-skinned man with a mane of blond hair. This was not, however, his true form; he was actually some sort of weird, tentacled, plantlike thing.
Lucifer, as he appeared in The Sandman and his self-titled series, was also a tall, blond man. This version of the character was pretty clearly inspired by Milton's Paradise Lost. And by tall, blond man, we mean that Neil Gaiman ordered the artists who drew Lucifer to make him look like David Bowie.
The store owner's son Dennis in Cabin Fever is more a case of "Blonde Kids are Psychotic", as can be seen in this scene. Jeff is also blond and quite frankly a dickhead. He takes off into the woods on his own, leaving the others behind to die.
In American Pie, the four main guys are all dark-haired and (somewhat) sympathetic. And then there's Stifler.
James Bond faces muscular blond henchmen on a regular basis:
Dr. Curt Connors The Lizard received an Adaptation Dye-Job in The Amazing Spider-Man. The burglar who shoots Uncle Ben is also shown this way, but was blond in the comic that first introduced Spidey as well.
Any villainous character played by Dolph Lundgren, but specifically Ivan in Rocky IV and the badnik in Universal Soldier. It's probably also worth noting that the only two antagonistic boxers that Rocky faced who were white were both blond, the other being Tommy Gunn.
About 80% of all the characters Mark Rolston has played. (The other 20% were just assholes.)
Jake Busey and his father, Gary, are both ash blond, and both play bad guys fairly regularly.
Genesis from Suicide Club is horribly evil, and happens to be the only blond in the whole damned thing.
The TV movie She Cried No starred Mark-Paul Gosselaar as a blond frat boy who rapes innocent freshman Candace Cameron.
Possessive ex-boyfriend who won't accept that it's over Cole Whittier (Robert Prescott) in Bachelor Party (1984) versus witty and easy-going brunet Rick Gassko (Tom Hanks).
The members of the heist are all assigned color-based code names, and of the lot, only "Mr. Blond" is outright evil, although he isn't actually blond-haired.
The only blond character is Nice Guy Eddie (although it looks more like red hair at times). Total Jerkass.
And Tim Roth's hair is sort of dirty blond/lightish brown. Symbolism?
In Never Back Down, brown-haired Jake Tyler fights blond Ryan McCarthy, who's fond of luring people to his home under false pretenses and savagely beating them.
One of the most famous examples of this trope is in The Karate Kid. Dark-haired Daniel Larusso (Ralph Macchio) battles Johnny Lawrence (William Zabka, career Evil Blond Guy) for the affections of fair-haired Ali Mills (Elisabeth Shue). All but one of the main Cobra Kais are blond. None of the blond guys in any of the movies are nice.
Zabka played another bully the next year in Just One of the Guys and one final time the year after that in Back to School.
In The Dark Knight, brown-haired Batman battles blond baddies. The Joker's hair is so greasy it looks dark, and cheaply dyed green on top of that, but he's definitely blond. Like Bruce Wayne, Harvey Dent suffered two terrible losses and assumed a new identity. But while Batman dedicated his life to fighting crime, Two-Face tried to kill a cop's innocent child.
Harvey Dent was an interesting subversion (or untwist) of the trope — the angsty, brooding dark-haired hero mopes as his love-interest takes up with a blond, popular, media-savvy politician who wears his idealism on his sleeve. Surely, the blond rival must be a superficial jerk, incapable of truly loving the heroine and only affecting high principles for show? No, it turns out that he really is a courageous, noble, if somewhat vain man and a better match for the girl than the hero, until the poor blond man gets broken to pieces in the most horrible way.
Justin Long is Accepted by Blake Lively after she realizes she's in another Hollywood love-triangle where the blond guy turns out to be a jerk.
Cary Elwes's oh-so-British Captain Boone competes for the affections of Lena Headey with Jason Scott Lee's sensitive, dark-haired jungle boy Mowgli in the 1994 live-action adaptation of The Jungle Book. He's evil, just so you know.
Cary Elwes is also evil in Twister, opposing brown-haired Bill Paxton. (Who, in a further demonstration of this trope, dyed his hair blond the following year as a morally ambiguous treasure hunter in Titanic.)
In She's All That, knowledge of this trope makes the plot's climax and eventual resolution very predictable, since male leads Zack and Dean are, respectively, brunet and blond.
In Die Hard, the only noticeably blond characters are two of Hans' henchmen (who are brothers). And in the third film, Hans' own brother is blond.
Vigo the Carpathian from Ghostbusters II (played by the younger brother from Die Hard).
Valentine from the oh so wonky film MirrorMask has dark hair, but wears a mask that has blond Bart Simpson-like "hair". It covers part of his natural dark hair. In the film, Valentine is shown to be a really friendly, helpful guy, even successful (owning a tower and such). Near the end, he sells out the main character Helena for all the jewels he can carry. His dark-haired side soon wins out and his guilt causes him to come back for her, though it's never told whether he gives back the jewels.
Greg Marmalard in Animal House is the head of the Omegas, the prick fraternity that is out to shut down the Deltas. On the other hand, the Deltas are chaired by the blond-haired Hoover, who spends the whole movie desperately trying to keep his fraternity from getting kicked off campus.
In Real Genius, William Atherton (Prof. Jerry Hathaway) and his brown-nosing sidekick Robert Prescott (Kent) constantly try to thwart, and later steal, the hero's invention.
In Revenge of the Nerds, Stan Gable (Ted McGinley) is head of the Alpha Betas, a sadistic-jock-filled fraternity. He torments the titular Nerds for most of the picture, until he learns his lesson after Lewis Skolnick (Robert Carradine) heroically rapes Gable's girlfriend in a funhouse. (Ah, the 80s.)
Gage, the little blond kid from Pet Sematary. He put the 'Evil' in 'Evil Dead'.
The bleached-blond black dude following Leana Telfer around in 1999's thriller The Ninth Gate.
The blondest guy in Road Trip is Jacob (Anthony Rapp), so it should come as no surprise when he does everything he can to thwart the fair-haired Beth from hooking up with sensitive brown-haired Josh Parker (Breckin Meyer). Jacob even impersonates a teacher to make Josh miss an important test.
The Devil Wears Prada confirms that in any love triangle, dark-haired men like Nate (Adrian Grenier) are caring and compassionate, if overlooked, while blond men like Christian (Simon Baker) are knaves who only seem like a catch until their untrustworthy shenanigans are exposed.
In Adventureland, Em (Kristen Stewart) is torn between the awkward James Brennan (Jesse Eisenberg) and blond, musically-inclined repairman Mike Connell (Ryan Reynolds), who claims to know Lou Reed. Ladies, here's a hint: always go for awkward. The audience soon learns that the only connections the married repairman has are with a string of underage girls.
Played extremely straight in 220.127.116.11 where the only notable male character with (vividly bleached) blond hair turns out to be a thief and an evil would be rapist.
In Super Mario Bros., King Koopa (Dennis Hopper) is blond, which makes sense because, in the video game, he is a reptile. With red hair.
Labyrinth: The Goblin King has pale hair, wants to turn a baby in to a goblin, and pulls some nasty tricks to keep Sarah from getting through the labyrinth in time. Technically, he doesn't break the rules, since the only one is 'get through the labyrinth in time', but it's still slimy behavior.
The whole trope was probably jump-started in movies by Alan Ladd, playing the Anti-Villain Raven in This Gun for Hire (1942). Ladd started off the film with black-dyed hair, but the dye job was abandoned about halfway through. He went on to play a series of rogues, rebels, and shady characters until "Touched by Technicolor" in 1949.
Dune: Paul is dark-haired, as was his father, Feyd has a reddish-tinged blond thing going, and the Baron is a redhead who leans toward blond.
Dr. Zaius in Planet of the Apes is a blonde-haired orangutan and the main antagonist, despite that he doesn't look so threatening.
Played straight in the 1990 film of Lord of the Flies where both Jack and Ralph are given an Adaptation Dye-Job to become blond and brunet respectively. In the book, Ralph was blond and Jack was red haired.
Mark from Old School, considering his first scene is as the boyfriend of the girl that Mitch likes, it's pretty obvious what's gonna happen.
Although, as demonstrated by his final scene, Roy's not really evil. Just misguided.
Averted in The Legend of Bagger Vance: Of the two big-name pro golfers competing with Junuh in the tournament, Bobby Jones is the clean-cut blonde who, due to this trope, may at first be expected to be the cocky jerk—but he's actually very sportsmanlike, and came to respect Junuh and his game, unlike the more condescending dark-haired and less clean-cut Walter Hagan.
Freddy Krueger from the A Nightmare on Elm Street series, back when he was still a human serial killer. After his death his preferred form as the nightmare monster that he became was to appear in his burnt body, but he could assume virtually any shape he wanted.
Iron Man 3 has both a muscular Implacable Man blonde henchman in James Bond tradition, and Guy Pearce's Aldritch Killian.
Kyle from Beastly is a spoilt and arrogant jerkass who predictably gets broken. Big time. Notably in his beast form, he doesn't have his blond hair.
In the film of Ichi the Killer, sadomasochistic mob enforcer Kakihara is a bottle blond.
Sloane of Entertaining Mr Sloane subverts the trope. The blond bisexual Sloane initially seeks to play siblings Kath and Ed against each other but by the end winds up in sexual servitude to both of them.
The first Song of the Lioness book has Ralon of Malven, blond and blue-eyed. He grew up to be a rapist, was disowned by his family (and hideously scarred with acid), turned to a life of crime under the name "Claw", involved himself in the Big Bad's plot to assassinate the king, and got killed during the climactic battle. Joren's almost progress.
In the Angels Unlimited series, the antagonist, Brice, has a bleach-blond mullet. After he goes back to Heaven, he still dresses in black, but he cuts off the mullet, spikes it, and only dyes the tips blond.
Some of the minor Death Eater characters, such as Yaxley, are also blonde.
Gilderoy Lockhart. He's not a Death Eater, but he's definitely a jerk and a fraud. At the end of Chamber of Secrets, he tried to obliviate two twelve-year-olds and planned to leave an eleven-year-old to die, intending to spin a good story about it that will paint him as the hero and the three students as unfortunate collateral damage.
The Time Traveler's Wife invokes this trope twice over: while neither Ingrid nor Gomez (the blond romantic rivals to the central couple's brunet Henry and redheaded Clare) are bad people, the former is needy and confrontational and the latter is offputtingly glib and cynical (and has a weird and severe Communism fetish). Neither Henry or Clare view them as legitimate contenders in the Love Dodecahedron (although Henry and Ingrid dated before he met Clare).
The villain of Hogfather, Mr. Teatime, is blond and generally possessed of youthful good looks apart from a creepy eye. He's also a Psychopathic Manchild and one of the worst villains in all of Discworld. Even the Assassins' Guild don't really want him around.
William Vanderveen of the Ryan Kealy book series fits this trope perfectly. He's blonde, incredibly attractive, seems eternally youthful, had an IQ of 180+ when he was about eight, and is out to destroy America and the rest of Western civilization because his sociopath of a father died when the CIA pulled support for political reasons, his mother committed suicide, more likely than not also influenced by the loss of their daughter/his older sister, who young William himself killed for having less than discreet relations with a local South African. So...yeah.
In Morpho Eugenia by A. S. Byatt (filmed as Angels And Insects), this applies to both men and women: the dark-haired protagonist marries into a blond-haired family which is obsessive about bloodlines, dark secrets are uncovered, and he leaves town with a brunette.
Nicolae Carpathia, the Antichrist in the Left Behind books. Also, Lucifer himself, as shown in one scene in Glorious Appearing.
Warner in Shatter Me, who wants to use the main character whose touch is fatal as his weapon.
In John le Carré's "Call for the Dead" a German agent is killing people to cover their tracks. He does not use his real name and makes his contacts give him a nickname to use. He is then called "Blondie".
In Firebird (Lackey), Ilya may be the only exception. His father and his brothers are all jerks.
In The Silmarillion, Celegorm is the only one of Fëanor's seven sons to have blond hair, and he's arguably the worst of them (admittedly none of them are particularly good people). Averted with his cousins the children of Finarfin, however.
In The Kite Runner,the bully rapist, and pedophile Assef is blond. He believes he is superior, because he is half German (and is a self-proclaimed Nazi) and Pashtun, the majority ethnicity in Afghanistan.
Spike. He's probably intentionally invoking this trope (the guy's pretty Genre Savvy); flashbacks reveal his normal hair is mouse brown and curly. Apparently, he dyed his hair black during WWII and began bleaching it in the 70s, probably to attract dumb victims drawn to the "bad boy" association.
Lothos. In the movie, he is played by Rutger Hauer.
On Dexter, Rita's abusive, drug-addicted ex-husband Paul is blond, contrasting with his former wife.
That actor (Mark Pelligrino?) could be the poster boy for this trope, since he's always evil (although it's arguably due to his looking and acting distinctly working class, in series written by and aimed at middle class audiences, not his hair coloring). He even played Lucifer on Supernatural,
Prince Joffrey, Viserys, and Jaime from Game of Thrones fit this trope, to varying degrees. Especially Joffrey.
Vim Fuego/Alan Metcalfe from The Comic Strip Presents...episode Bad News has a huge rock-star mane of blond hair, and while he isn't evil, he is arrogant, obsessed with his own talent, violent, not above fraud, and arrogant.
Edie's new husband on Desperate Housewives was fair-haired, pale eyed, and extremely creepy. There was no doubt he was evil from the second he appeared onscreen, even though it had yet to be revealed what he was actually up to.
This trope is a staple of Hispanic soap operas, though it usually applies to women rather than men.
Alexander Lucard from Dracula: The Series. Guess who he was?
The O.C. had Kevin Volchok. But it also has good blond guys (Ryan Atwood) and bad dark-haired ones (Oliver Trask).
One Tree Hill did it exactly the other way around: blond Lucas is the good (half) brother while black-haired Nathan is more of a bad boy.
It's nearly a trope on Hogan's Heroes. If there is a (male) prisoner, Allied soldier, or member of the underground with pale blond Aryan hair, he's almost certainly a spy.
Eric from True Blood is the ultimate badass blond: he's a Viking vampire, sheriff of his corner of Louisiana (for the vampires) and owns a nightclub called Fangtasia. He becomes upset when he gets blood in his beautiful, blond hair.
The Master, in the Christmas 2009 finale, has a new-and-improved blond look and a whole new load of crazy to dump on the Doctor.
Mark Gatiss wears a blond wig to play Prof. Lazarus.
The Editor, played by Simon Pegg in 'The Long Game'
While the Sixth Doctor is not evil, he's by far the blondest of the Doctors, and by far the most Jerkassy and egotistical of the Doctors (with the exception of the First Doctor's Early-Installment Weirdness phase). He possesses very striking, brilliant yellow-blond hair to contrast with his previous regeneration's more subdued, natural dark blond, him being by far the most noble and selfless Doctor. All other Doctors have either dark or grey hair.
John-Paul McQueen from Hollyoaks drove his ex-girlfriend to anorexia, had an affair with his friend's boyfriend, convinced a priest to leave the church, then later left said priest for another bloke. Also, Ste Hay is blond.
In the short-lived BBC kids' drama Dark Future, all the villains of the story were blond. Out of the trio of schoolaged heroes, the two girls were both brunette. The villains at one point try to draw the young blond male hero into joining their cause, but then turned on him when they found out...his hair is naturally a dark brown, he just dyed it (which should've been obvious, his dark brown roots were even visible!).
In the pilot of the Stephen King series Haven, Ted, the blondest guy in town, turns out to be a con-man and accomplice to murder who was pretending to love a woman for her money.
Baby-faced Jadeite in Pretty Guardian Sailor Moon. Of the Shitennou, he's the only one whose dedication to Beryl does not waver during the whole season. The sissy villainy also pops up in the Episode 0 special, as Jadeite's actor plays a female/crossdresser (it isn't clear which).
Justified has Robert Quarles (played by Neal McDonough), a sociopathic mob lieutenant.
"Jessie", from Rick Springfield's music video of "Jessie's Girl", is blond.
The music video for Muse's song Knights of Cydonia has a heroic dark-haired cowboy fighting with an evil blond cowboy over a blonde woman.
Angelspit's "Devilicious": "If you're needing a villain, baby, I'm your blond".
In a meta example, early Visual Kei rockers in The Eighties and early in The Nineties were known for shocking appearances, drama, fighting, violence, insanely heavy drinking, and huge, dyed-blond hair. Many Japanese bars as a result at the time would post signs banning specific offenders (such as "No Yoshiki!") but others had a blanket ban on blonds entirely, with "No blondes" or "No funny hair" type signs.
Presumably invoked by Scott Steiner: when he turned heel at WCW SuperBrawl 1998 and joined the nWo, he dyed his hair blond to accentuate his turn. He stayed a blond for the rest of his career afterwards (through good and bad).
In Spring Awakening, the basic idea is that all the children are good and naive and the adults are evil. However, there is an exception to the lovable children: Hanschen, the Aryan seducer and predator who creeps everyone out and seduces this poor, awkward guy, Ernst, who has a desperate crush on Hanschen. Even though this takes place in GERMANY of all places, Hanschen is usually the sole blond. Word of God has confirmed that this trope is being invoked on purpose (and so one assumes that the dark-haired Hanschens, understudies aside, are only that way because they couldn't pull off the desired blond).
Brett, the Jerk Jock in 13, was played by the blonde Eric Nelsen.
Anogia from Luminous Arc 3 played this really straight, until it is revealed that all he went through is to give Miria her eyes back.
In World of Warcraft, Arthas Menethil, a prince who would later kill his father and become the villain for the third expansion pack Wrath Of The Lich King, is blond (though in undeath, his hair turns white). In addition, Prince Kael'Thas Sunstrider is also blond.
Geese Howard, the first SNK Boss. There's also Rugal Bernstein, the successor to the mantle. Interestingly enough, Geese is killed by a blond guy, Terry Bogard, and his son Rock is blond (with red eyes to boot). The Big Bad of Mark Of The Wolves, Kain R. Heinlein, also has red eyes and long blond hair. It's not a coincidence or anything; Kain is Rock's Evil Uncle and Geese's brother-in law. Poor Rock. He knew Kain was half-evil, but then he found out the other half was evil, too...)
Even worse, there's Colonel Volgin who's possibly one of the most purely evil characters in the entire series and whose theme is called "Clash with Evil Personified". Naturally, he's blonde.
Gene is a twisted manipulator who intends to create an even more abusive version of Outer Heaven then Big Boss and is also blonde.
Though Ocelot was introduced old and grayed, when he was young he was a blonde traitor to start with.
Currently retired Bigger Bad Zero who is behind the creation of the Patriots that secretly manipulated the world for almost half a century is also, of course, a blonde. Are you suspecting a pattern here, or what?
The aptly named Mr. Blonde in Perfect Dark. Yes, it's a pseudonym and as a matter of fact, he's not really blond; the reptilian aliens mustn't have been trying very hard, because they all use the same holographic disguise.
None of the all-blond Branstein clan in the Super Robot Wars franchise are actually evil, although you are nominally fighting against Maier and Elzam at the beginning of Original Generation, Rai is kind of a jerk, and Elzam is an Aloof Big Brother (and A CHAR).
The Silencer from Crusader is revealed as blond in a rarely-seen death animation. A half-subversion in that he is the protagonist, but even if he isn't evil, he is far too willing to carelessly shoot unarmed surrendering civilians for no reason.
Dane Vogel from Saints Row 2. Potentially the player character as well.
In Final Fantasy IV, the original SNES version, Kain is shown to have blond hair in the game's ending (it's the only time his helmet is removed, and it doesn't show in his menu portrait). In the remake, his blond hair is more prominently displayed. It might be argued that Kain isn't really evil, but as Golbez noted, those that were taken over by Zemus/Zeromus had evil in their hearts. Kain's jealousy over Rosa loving Cecil and not him is what made him willing to turn against his friend. Also, he doesn't have a problem with using brute force to get something done—he says as much to Cecil when Rydia is unwilling to go with them after Mist is burned.
In Final Fantasy XI, you get the villains the two Zilart princes of Jeuno, specifically the older brother, who is actually behind the first villain for the first expansion and Nag'molada for the second.
You can see that the bad guy, Dysley, in Final Fantasy XIII is blond. Don't look at his headdress, look at the hair on his back.
Inverted in Final Fantasy XII. Straight-up heroes Vaan and Basch are both blond. Balthier has light brown hair, and is rather abrasive, but not evil. The Big Bad, Vayne, has dark brown hair.
Zephiel and Guinevere's dad, King Desmond, is revealed in the prequel to be a major Jerk Ass who attempted to kill Zephiel at least twice, and is pretty much responsible for Zephiel becoming a villain in Fuuin.
Jin Kisaragi. He's an aloof, nihilistic, and borderline sociopath who doesn't hesitate at all to belittle those weaker than him, or cut them down if he feels they are impeding his progress. He's outright homicidal around his brother or lieutenant due to his Evil Weapon warping his mind. He softens up a bit after overpowering said Evil Weapon, and focusing his efforts towards saving his childhood friend/Implied Love Interest from the enemy's side, and even then he's still a jerk.
Relius Clover, Mad Scientist extraordinare who turned his daughter, and later his wife into automatons without any tinge of remorse. He's not only one of the series' major antagonists, but he sees people as nothing more than things to be experimented on and these experiments aren't humane to say the least. He also happens to have a son...
Carl Clover, a sweet and caring boy traumatized so badly by Relius' experiments on his beloved sister that he lost part of his sanity. With the assistance of the Nox Nyctores Nirvana, his emotions were suppressed, and his overall mistrust of people (adults especially) causes him to take some questionable paths towards his goal. These include calmly threatening people with death, especially those who refuse to give him information. He even alludes to knowing methods of torture to extract said information. But ultimately, Carl is a subversion. His Character Development leads him towards a path of helping others in need, while keeping to his more noble pursuit of saving his sister, while aiming to avoid becoming like his father. Despite being coerced to work with Relius in CP, he works hard to become nothing like his father.
In the arcade version of Double Dragon, Billy has blond hair while Jimmy has brown, even though both are technically good guys. When Jimmy was turned into the main bad guy in the NES version, he underwent an Adaptation Dye-Job and had his hair color switched with Billy's, becoming a blond guy in the process.
Ludger Brink in The Dig, playing against dark-haired astronaut hero Boston Low.
Slade from Heart Core. The man is so damn evil that he strikes fear into even the strongest demons just by being near them. He is even willing to kill his own allies for fun and curiosity and it is also implied that he has plans to betray Royce.
The website hosting the Nukees comic also includes a page dedicated to SUSBEC: tracking evil, eyeless blonds, mostly male.
The titular protagonist of Niels, a violent, sociopath mob boss, is blonde. So is Peter.
In Voodoo Walrus, Cyradwee, Shmeerm, and Rip Flintlocke all follow this trope. Actually, it could be argued that Shmeerm is on the fence. We haven't seen him really do anything particularly evil in a long time.
Amical from morphE is a cute gentleman with beautiful golden curls... and a magical flintlock pistol which he kills 3 people with before the end of the first chapter.
In the DVD commentary for the Futurama episode "Anthology of Interest II" wherein Bender is turned into a human, it's stated that Mili Smythe "insisted that Bender be a blond man" as "blond men are more disgusting".
Episodes of Cadillacs and Dinosaurs typically revolved around some sort of conflict between the jet-black-haired (and heroic and environmentally-conscious) Old Blood Mechanic Jack Tenrec and evil Poacher Hammer Terhune, whose most prominent physical feature was his enormous, blond flattop mullet. Additionally, perhaps the only other blond male character to appear was Shawn Russell, another Old Blood Mechanic who, in direct contrast to Jack, was depicted as being arrogant, corrupt, and greedy to the extent that he was willing to betray everything the Old Blood Mechanics were supposed to stand for.
Hey Arnold! averts it very hard with Arnold, who is one of the nicest characters on the show. It does, however, play it straight with Wolfgang and Edmund, as well as with Olga Pataki's con artist fiance Doug.
Boog from Fanboy and Chum Chum is also a blonde bully - however, he evidently uses dye, since, at the time the show takes place, his brown roots are quite visible.
Bart Simpson of The Simpsons. (Or Anti-Heroic, at the very least.)
Geoff of Total Drama, while being the host at Total Drama Aftermath. He got better, though.
Regular Show has a group of blondes with whom Mordecai hangs out after dyeing his hair in a bet with Rigby that turns out to be a Blonde Superiority Cult that believes theirs to be the best hair color, to the point where their initiation ceremonies consist of forcibly dyeing an outsider to death with boiling hair dye.