There is a fic in which Syaoran from Cardcaptor Sakura grew up to be a wife beater, and Tomoyo called in a favor from her mother to have him killed in a hit-and-run. Also, at the height of Eriol/Tomoyo's popularity, it was not uncommon to find fics where Kaho, Eriol's official Love Interest was put through a Humiliation Conga that only started with Eriol dumping her for Tomoyo amid cheers from the rest of the cast. One particularly ridiculous fic gave the "justification" for all the torture that Kaho was too tall for Eriol. Yes, a woman being taller than her boyfriend apparently makes it all right for everyone to abandon her when she's kidnapped.
In Dragon Ball Z fanfics, Yamcha and Chi-Chi are bashed mercilessly, and sometimes, even Bulma, Videl, and Goku fall victim to this.
In the G Gundam fandom, a certain revenge fic was once written to "counter" or "parody" the George x Chibodee yaoi fanfiction by showing how bad they'd get along if they had to move in together. The fans "loved" it, but technically... it' didn't work as well as intended. The pairing bashing and how the fic came from a blatant hater of the couple gave all away.
The Love Hina fandom sees this treatment pop up periodically for Naru, Motoko, and Kitsune as a result of their canonically abusive and exploitative treatment of Keitaro. Some authors extend this to include Su, Hina, and Haruka, the latter two primarily due to their manipulation and indifference to Keitaro's plight respectively.
A lot of fics seem to revolve around Naruto getting revenge for his initial status as Butt Monkey in the first couple of arcs. Even though things improve for him later on in the series, some angry Fans cannot seem to let go and either refuse to acknowledge or completely reverse the positive changes in his treatment.
Setting the filter to Sasuke and searching the term Bashing on Fanfiction.net gives you seven pages worth of character demolition, "hilarious" pranks, and terrible grammar. They tend to give him a characterization of heartless monster, misogynist, impotent, trigger happy, cowardly, backstabbing, whiney emo bastard. The Kicker? Itachi was often put as a good guy/love interest at the same time, before there was even a speck of redemption for the character or any alternative interpretation whatsoever. Right after he brutally beat and tortured two protagonists, there was a flashback of the Uchiha Massacre and tried to capture/mutilate Naruto. And there are Flame Warsby many who state that this is canon.
Sakura is attacked without mercy. Just about every character in Naruto has been subject to a Hate-Fic, but not as many as Sakura. In the Fanfic Darkness Within, you can see how much the author absolutely hates Sakura and, to a lesser extent, Sasuke. The author wrote it out of frustration and was completely shocked on how many positive reviews it got. Even more egregious is how they tend to ignore all Character Development she went through during the Chunin Exams and the Time Skip, keeping her as a weak, Sasuke-worshiping load who drags the whole team down, despite the fact that she became an incredibly competent Medical Ninja during the Time Skip with strength that Rivals that of Tsunade herself.
Neji tends to escape unscathed from this despite his first major appearance had him straight-up attempting to KILL his cousin for a reason that basically amounts to "getting kidnapped by a Jounin-level spy when she was three", even though there were several OTHER (much more valid) targets for his rage other than his little cousin. In fact, most of Team Gai escapes from this, Team ten (excluding Ino) as well.
Many authors love to add to Naruto's backstory a history of open, often murderous, physical abuse by the people of Konoha. In addition to all the revenge necessary against the village as a whole, this often results in a Plot Tumor in which all the people who should be responsible for keeping an eye on Naruto — the 3rd Hokage, Kakashi, and Jiraiya — are called out as incompetent, cowardly, or callous.
Despite being an excellent writer overall and one of the most popular writers in both fandoms, Matthew "Viridian" Schocke has a tendency to do this in his Harry Potter and Naruto fics.
Kakashi also gets a lot of malice for perceived favoritism towards Sasuke over Naruto. The worst part is that Kakashi only did it once and it was justified(He also left Naruto with a guy who became Jonin because of his teaching abilities, and ended up leading Naruto to his other mentor, Jiraiya. And of course, the fact that if he HADN'T taken the month to train Sasuke, he was pretty sure that his fight against Gaara would have killed him).
Naruto himself is not immune to this. One particular fic for example decided to strip away every characteristic except his love of ramen. The result was a morbidly obese Naruto who's both lazy and a complete coward. It's particularly jarring when Haku (one of Naruto's first friends in canon) outright hates Naruto specifically for being fat.
Hinata also gets a lot of flack for her perceived Stalker with a Crush tendancies, her perceived spinelessness/weakness, and her inability to admit her feelings for Naruto. Many authors who do this tend to ignore her often mentioned past where she was psychologically destroyed by her father for her inability to master her clans techniques (she is rather adept at them, managing to briefly match her prodigious older cousin Neji in their Chuunin Exam match). Fics that do this tend to exaggerate her shyness and portray her as a spineless coward who relentlessly stalks Naruto.
This often happened to Shinji from Neon Genesis Evangelion, possibly because the authors saw too much of themselves in him. Of course, since he's from Evangelion, Canon wasn't especially nice to him either, but still...
Those who don't hate Shinji will often take their rage out on his dad. There are a number of stories that involve Gendo being brutally murdered or at least humiliated for treating his son like dirt. Sometimes through turning Shinji into a Possession Sue.
Ranma ½ has this going on big time. The two most notable subjects, particularly in the sheer vehemence of what they suffer when one of these gets going, are Akane Tendo and Ryoga Hibiki. The latter even has an underground ring of fanfics where he ends up either permanently trapped in his cursed form and sent to a farm, or just butchered and eaten.
Sailor Moon fanfics where Sailor Mars and Tuxedo Mask betray Sailor Moon, pair up and declare their collective hate for her was/is depressingly common. This seems to be more common with fics based on the MacekreDiCanime dub than the original, which made Raye and Darien much more harsh than Rei and Mamoru. But ones based on the original do exist too.
The Tenchi Muyo! fandom has what is called AHRL and ALRH fans - short for "Ayeka-Hating, Ryoko-Loving" and "Ayeka-Loving, Ryoko-Hating" - whose fics tend to turn one girl into a raving bitch and another a virtual saint as they win Tenchi's heart.
Insane Rocket Shipper fan and author Cori Falls is legendary for these.
In The Grinning Snake, a crossover between Mai-HiME and Hell Girl written by someone upset over Shizuru not suffering any consequences for her actions, the daughter of one of the people Shizuru killed in her attack on First District Headquarters, after uncovering evidence of her guilt and failing to get Shizuru charged with murder or hear any true remorse from her, enters into a contract with Enma Ai to send her to Hell, making it also a literal revenge fic.
The second variety was both named and typified by the Revenge Wars which flooded the Anime Fan Fiction Mailing List in response to and in the wake of Scott "SKJAM!" Jamison's story Sauce.
The Lord of the Rings movies triggered a series of fanfics portraying Arwen Evenstar as a vindictive, vicious, shrieking harpy who seduced Aragorn so she could become Queen of Gondor. This is generally perceived as an expression of resentment over Arwen's having "stolen" Aragorn from his true love Éowyn, his real true love Legolas, or his real real true love, Marisuthiel.
And then there were the ones written by the people who were upset about her stealing Glorfindel's role from the books.
Doctor WhoExpanded Universe writer Lance Parkin once posted one of these to Outpost Gallifrey about a character everyone probably knew he hated anyway, seeing as he turned into a Designated Monkey whenever Parkin wrote him. Yeah, man, way to show that fictional character, spending your precious time writing two novels costarring him, nursing a grudge for two years, and writing a little story about him getting hurt in a nasty way. You sure showed him! Ha ha, not.
Another example might be Ian Fleming getting sick of James Bond and killing him off at the end of the novel From Russia with Love; however, the book was so well written and so much interest generated in the character that this death didn't stick, either. It was never planned that way anyway. He'd already written Dr. No.
The War Against the Chtorr novel "A Rage for Revenge" has a lengthy section detailing the Humiliation Conga inflicted on a producer who ripped off his writer. Author David Gerrold thinks that anyone who pisses off a writer is just asking for trouble. "How many stories have you read that are basically about revenge?"
Garrett P. Serviss' 1898 unauthorized sequel to H. G. Wells' novel The War of the Worlds, Edison's Conquest of Mars. In this novel Thomas Edisonreverse engineers the Martian technology,combines it with a few inventions of his own to build a giant space fleet, and proceeds to fly to Mars with a huge army and beat the living crap out of the Martians with ludicrous ease. The entire book seems dedicated to inflicting as much pain on the Martians as possible, although the characters relent slightly near the end. Due to the lax copyright laws of the time period Serviss had no legal problems serializing or publishing the novel. H. G. Wells did not approve of the book. Thomas Edison did.
Smallville's Lana Lang had this. A lot. Let's just say that there were many Smallville fans who hated Lana's Mary Sue status on the show and were eager to take the character down a peg.
Jonas Quinn of Stargate SG-1 managed to accrue a lot of these fics in the single season he replaced the character of Daniel Jackson. People either love Jonas or hate him... and the scale is mostly tipped towards hating him.
Pick a crime show with UST. Any crime show. Now find someone who interferes with the aforementioned UST. There's fanfiction featuring them being tortured in some sadistic fashion if you look in the right places.
Buffy's unpopular love interest Riley Finn got a few of these, the most extreme of which featured Angelus returning to Sunnydale and skinning Riley alive while Buffy watches. The story ends with Buffy and Angelus making love on a rug made of Riley's skin.
Netorare is the Rule 34 way of responding to spineless harem males, or so some claim.
Not much of a stretch, considering the definition of Netorare is more or less "Sex with the faithful man rendered helpless to stop" in some way, via drugs, bondage or even taunting the victim though photos...
In Star Fox fics, Fox McCloud tends to earn the wrath of certain particular authors for breaking up with Krystal in Star Fox Command. Said authors tend to conveniently overlook the fact that he did it for benevolent reasons, that even he realises it was a stupid decision and is already miserable enough over it, as well as the fact Krystaloverreactedmajorly and is far from faultless herself. As well as the fact that Command is considered to have not happened. Many of them also tend to derail Fox, so that Krystal can be paired with the Author Avatar as well.
While fic torturing The Nostalgia Critic is likely the most popular genre in the TGWTG fanfic fandom, at least it's done with love and keeps the boy in-character. Not the case for "Beer Enema", which stars an evil second-person narrator mutilating a shell-like Critic whose only personality is being a Pretty Boy with no spine.
In the SCP Foundation, there were a series of SCPs that the authors decided they really, really didn't like. So they came up with heavily exaggerated stories detailing how the Foundation got rid of them, all involving very horrible ends for the SCPs, which became known as "decommissioned" SCPs. After this purge they decided not to ever do it again, lest writers create terrible SCPs purely in the hopes of getting awesome declassified stories.
The decidedly darker Wipe the Slate Clean opens with Meg killing Peter, Chris, Lois and a robotic duplicate of Stewie with a shotgun, then preparing to leave with Brian and (reluctantly) the real Stewie to Mexico. Subverted in that revenge isn't really the main point of the fic. The real point is more like Throw the Dog a Bone (for both Meg and Brian).
The King of the Hill: Peggy's Revenge fanfic by Joey Joe Joe Jr. Shabadu had Peggy, Lucky and John Redcorn going OOC to torture Hank because he's bad at sex.
There's a Phineas and Ferb fan fiction writer called "Blackspiderman". A long time ago, he hated Candace. And almost every single thing he wrote had Candace going through all this shit and sometimes some characters will go OOC to rage about her and her busting obsession. Yes. But now, he likes her, and has stopped writing revenge fics. and now he even considers them his Old Shame.
In the Total Drama fandom, Courtney is an especially common target for such stories by virtue of being one of the original cast's most polarizing characters.
Dakari King Mykan is infamous for only writing that kind of fanfiction in general. By June 2013 he has written over 150 fanfics, most of which center around him turning lovable characters of shows like ''Digimon'' and ''Teen Titans'' into jerkasses who hurt or kill their friends, because he is unhappy with the fact certain pairings got bombed (to the point that he claims the Teen Titans finale literally gave him PTSD). Thankfully he sucks so much, people who write MSTingsof his work told him to grow up and do worse to the characters than what he thinks is evil.
There's also The End of Ends which is this towards the finale of Teen Titans and doing almost exactly what the above described, with the added bonus of blowing up entire worlds just because one pairing came through while his preferred paring sank.
He even has a term for this kind of fic, "punishment fic," and has a certain commonly occurring variant. When one character (typically Davis or Beast Boy) doesn't get together with the one Mykan wants to pair him with (Kari and Terra, respectively), the former (yes, the person who got rejected, not the one who rejected him or the one she chose instead) will undergo a Face-Heel Turn and/or die, and the latter will be blamed for it. The aforementioned The Endof Ends is an example of this, as is "Cyborg Davis" (in which, curiously enough, Davis comes back to life and acts the same way toward Kari as Terra did to Beast Boy in "Things Change").
The Legend of Korra drabble You Killed Me is an unabashed one against Zaheer. (Whether or not villains have it coming is likely a separate discussion.)