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According to many movies, books, and TV shows, seriously good-looking men will usually turn out to have character defects making them just short of the Anti Christ. Polar opposite of Beauty Equals Goodness — originally a subversion of the trope, now has pretty much become a stereotype in itself. The Jerk Jock stereotype all grown up. In contrast, nerdy-looking or plain characters are usually nice.
Might happen because the authors are dealing with their own issues (ex-girlfriends or nerds). If it's the latter, the plain nice guy wins. If the former, then a fantasy idol who is an exception will be in the story.
Joe Bob Briggs discussed how you could tell the bad guy in thrillers. "For example, if you were watching the Lifetime channel, it was always the handsome guy."
Related tropes: All Girls Want Bad Boys, Man of Wealth and Taste, Evil Is Sexy, Bastard Boyfriend, Bespectacled Bastard Boyfriend, Handsome Devil. Often leads to a Draco in Leather Pants situation - he's an asshole but the female viewers/readers love him anyway. Compare Beauty Is Bad.
Rumiko Takahashi uses the variation Hot Guys are moronic buffoons, characters such as Mendou, Rei and Tatewaki Kuno are good examples. Rei is probably the best example as the Cute Monster Guy is so dumb he can only say a few words very slowly. Due to the artstyle they often don't look that much more attractive then the other characters.
Cruelly deconstructed in Sakura Gari, where the unearthly gorgeous Souma is a massive bastard... but he turns out to have an extremely complex reason to be an asshole. And his physical beauty brought him lots of abuse.
Animal House tries to have it both ways. The opposite number of Omega House's Gregg Marmalard is clearly Eric Stratton, who's just as handsome as Gregg is but is clearly intended to be the Designated Hero. But if you consider Gregg's "good" counterpart to be John Blutarski (who does ultimately succeed in wooing Mandy Pepperidge away from him, after all), then this trope is played straight.
Cruel Intentions: Both lead characters are played up as being very attractive, and both are rotten to the core. However, the film's climax features some character development for the male as he develops actual, honest feelings for the genuinely wholesome girl he was chasing for most of the film.
Joren of Stone Mountain in Tamora Pierce's Protector of the Small books, a misogynist asshole who goes to any length possible to get Kel out of knight training. According to Pierce he was based off of someone she knew in college.
Galad Damodred of The Wheel of Time was one of these. He was never evil per say but he would do what he thought was good, regardless of who got hurt. He got better in Book 13.
On the less sympathetic side, there's Rahvin.
In the second book of Kat Richardson's Greywalker series, the main character Harper immediately distrusts the really good-looking guy — she's right. Several other times played straight in this series. Harper winds up deeply in love with a guy who's not handsome.
Agatha Christie seems to have believed this very much. If a handsome man is introduced in a book of hers, he will be either the killer, the accomplice or otherwise immoral. Note that this is restricted to men whose attractiveness is spelled out: other characters might be handsome too, but the fact being mentioned is a sure sign that we're looking at a gigolo, a blackmailer or just a bastard. This is so prevalent in her writing that in the one book where a handsome man isn't a complete bastard (he's loyal and caring, but he still might be a gigolo), the killer turns out to be the other handsome man. This may be writer on board as Christie's first husband was a good-looking jerk.
Dr. Mark Ahriman of False Memory. Handsome, successful psychiatrist who mind rapes (and sometimes literally rapes) his patients, sending some out to kill people and driving others to creative suicide for his own entertainment.
Keifer Porter of A Brother's Price was noted for being cruel, dim-witted, and exceptionally beautiful. On the other hand, Jerin Whistler, who ends up marrying Keifer's widows, subverts this. He's noted in-universe for his beauty, and also for his intelligence and kind nature. Jerin even manages to help Trini deal with her aversion to men caused by Keifer brutalizing her before she was of age for marital relations anyway.
Joffrey Baratheon inherited his parents' stunning looks, but is physically and emotionally abusive to his family and fiancee and governs the realm with terrible petty decisions.
Gerold Dayne, also known as "Darkstar," has the traditional Valyrian beauty of the Daynes but is arrogant, mean-spirited, has a "cruel tongue," and is eager to make a name from himself distinct from that of his family. He's also not above nearly killing Myrcella, maiming her in the process if it means accomplishing that. For bonus points, Arianne describes the trademark Purple Eyes of House Dayne as looking black from a distance on him.
Downplayed with Loras Tyrell, whose trademark Tyrell good looks have garnered him plenty of In-Universe fangirls. He's arrogant and cocky, but isn't really a terrible person. And then he gets several major injuries attacking Dragonstone — having boiling oil poured on his face included — so it remains to be seen whether he'll live to subvert or invert this trope or not.
The series also inverts this by having more unattractive guys as more decent, such as Ned Stark or Tyrion Lannister, but also averts this by having good-lucking nice guys such as Garlan Tyrell and Robb Stark.
In the Heralds of Valdemar series, Herald Talia's abusive father and brother were quite attractive, and as a result she's wary around handsome men; the man she falls in love with is repeatedly described as homely.
Eric from True Blood, especially after he took a level in sexy in seasons two and three.
And Bill and Jason have had their moments of complete bastardry, too.
Prevalent in Supernatural. As a general rule, while a character's level of attractiveness doesn't determine how "good" they will be, the less attractive male characters seem to form better romantic relationships.
While Sam and Dean might basically be good people (at least, when Sam hasn't gone darkside) they both manipulate women for sex and have a tendency to self-obsess and act like major jerkasses to everybody around them. If you were a random bar-frequenting woman in the Supernatural universe and they hadn't saved your life, you'd be forgiven for thinking they were bastards. It's worth noting however that Sam averted this entirely before he became a Hunter again in the series pilot, instead having been in a stable and loving relationship with Jessica at the time.
Castiel isn't sexually manipulative towards women, but that might have more to do with his general cluelessness about human behaviour, his devotion to his faith, and disinterest in the matter. The sexual chemistry with Meg seems to be based around violence, and he once accidentally burnt somebody's eyes out and forgot to fix them, although it seems like he could have done so easily. So he's probably not the best boyfriend material, either.
Bobby is comparatively less attractive but was able to maintain a stable and loving marriage for many years.
While Samuel Winchester, Senior (the grandfather) is morally ambiguous, his marriage and commitment to his family seems a lot stronger than John's.
The only notable exception to the rule is Jimmy (Castiel's vessel), who is very pretty and was (before he became involved in angel business) a devoted and loving father and husband. And the actor who plays him is probably cuter when he plays Cas, anyway.
Almost every female demon, ever.
The Big Bang Theory. The series's Official Couple is pretty much set up to be the classic 'Nice Guy nerd courting the Prom Queen'. As such, almost, but not all, rival love interests who happen to be attractive, or at least arguably more attractive than Leonard, tend to be complete and utter assholes, who treat Penny terribly. The exceptions being Stuart (who goes from slightly adorkable Nice Guy to almost a parody of the Adorkable Woobie types), Zack (who despite fitting the mold, he's an example of Good Is Dumb), and her recent British study partner Leonard was jealous of, who was wiling to play along with Leonard's attempt to scare him off.
X-Men: Evolution used an art style that made most characters attractive. However, according to some fans, the most attractive characters are Pietro, Gambit, and Avalanche. While Gambit and Avalanche both have lines they won't cross and times of heroics, they still had strong shades of criminal level jerkery. However, Pietro takes the cake. Sociopathic disregard for human life? Check. Starscream level cowardice? Check. Draco level smugness? Check. Pretty white hair and bishonen level attractivness according to girl fans? Check.
The jock Duncan took Jerk Jock gig even further when he attacked the Morlocks with guns and bombs.
Eiichiro Oda appears pretty fond of it. Especially Nami and Boa often use their looks to get work done for them or get through with absurd actions.
Asuka Langley Soryu from Neon Genesis Evangelion. In spades. However, in her case, it's a brutaldeconstruction of this trope: she's a hot bitch, yeah, yet not only she doesn't get away with her antics (Touji is annoyed to no end by her, Shinji puts up with it because he's deeply fucked up, Rei is indifferent most of the time, etc.), but she's subjected to an horrifying Break the Haughty process that reveals her terrible Dark and Troubled Past.
As a possible example of this trope, there's one Nodwick strip in which a villainess explains her face (and gender) is always hidden because only hot evil chicks are allowed to show they're evil.
Double lampshaded because at first they just think it's because she was horribly disfigured in an accident, but then she mentions that even before the accident, a woman who was "nothing special" would have been a pretty good catch compared to her.
In Teen Girl Squad, Cheerleader is considered the hottest out of the group in-universe. She's also the meanest.