Ship wars abound in anime and manga fandom. The presence of DFOS is almost guaranteed in any case where The Protagonist has multiple love interests. Some shows have even gotten bad enough to warrant their own pages:
Aoyama Masaya of Tokyo Mew Mew, Ichigo's canon love interest. Fans who prefer Ichigo with the Jerk with a Heart of Gold or the Stalker with a Crush often portray him as either an unimportant idiot who is quickly discarded or an evil mastermind who is cheating on her with Miwa or Moe or both. (Or Minto in a double pairing derailment, if the shippers happen to come from the section of the fanbase that believes Yuri Is Ew.) Either interpretation completely ignores his kind, intelligent, loyal canon personality. He usually ends up run over by a semi.
It gets so bad that fanfic writers change the continuity so that Ichigo's Mysterious Protector, the Blue Knight, a.k.a. Ao no Kishi, turns out to be Ryou instead of Masaya, despite this completely destroying the continuity. Then again, that's how 4Kids did it, too.
Some of the less mature fans like to make Guido from Samurai Pizza Cats an abusive jerk because they see him as a threat to the Speedy/Polly pairing. This is ridiculous because Guido never shows any interest in Polly. For that matter, until the Grand Finale, neither does Speedy — they only fought over the affections of Lucille until Speedy fell for Polly at the eleventh hour. When Polly and Speedy do hook up, Guido is happy for them. The crazy shippers seem to hate Guido for being there, even though his lack of interest means that he's not an obstacle.
This happens from time to time in Ojamajo Doremi. Shiori and Fujio are sometimes this for Hazuki × Yada fans and there is some decent-sized Ship-to-Ship Combat between Kotake × Doremi, Akatsuki × Doremi fans, and Doremi-yuri-pairing fans. Imagine how the fans reacted when Aiko was given a Love Interest in Naisho where she neither admitted nor denied attraction to him, causing an uproar from fans who paired Aiko up with Nobuko/Momoko/Onpu/Leon.
Pretty Cure fandom is usually rather light on this trope, as most shows in the series have no canon pairings to begin with. However, when there are canon pairings, this trope can crop up. For example:
Kouji and Natsu from Yes! Precure 5. The fact that they turn into Talking Animal sidekicks Coco and Nuts spurred the hatred by providing Squick as a ready excuse. They eventually found fandom support, however.
Still from Doki Doki: ever since it was revealed that the movie is about Mana's marriage, Yuri Fan began to hate every single potential Love Interest of Mana. Nikaidou, one of Mana's classmates, got it especially hard ever since one of movie trailers showing him being all flustered when Mana gets close at him. And let's not get started on how he's treated in the last two episodes.
A minor example in the Magical Girl Lyrical Nanoha fandom: Frequenters of the AnimeSuki forum would've known the infamous 300 YU-NANO AGAINST LEGION OF FEI-NANO Flame War. And no, we're not talking about some smelly old men. This Flame War was mostly fueled by irritation that Yuuno was used as a plot device and not a character — an 'out' for the writers in case they got too scared of Nanoha/Fate. The Theme Park Version of this irritation is Yuuno Hate (at least from the Legion). But Poe's Law and GIFT means there are people who will take it seriously or claim total seriousness.
Even though Erio has managed to escape the brunt of bashing due to being overtly shipped with Caro, preventing him from being a threat to the main pairings, he still gets "Erio must die" vitriol every now and then from Het is Ew fans who think his mere presence among the main cast ruins the perfect yuri dynamic of the Improbably Female Cast.
This is common in Tenchi Muyo!, if for no other reason than the characters are usually already doing it themselves:
Sakuya Kumashiro from Tenchi in Tokyo was added in as a third love interest, and was actually picked over both Ryoko and Ayeka, leading both fan segments to hate her, which leaves her with very few fans. She didn't make it to the end of the series, though.
And all of this is incredibly ironic since the Word of God has stated that Tenchi eventually just marries them all. Of course, some people just ignore that as well.
Considering that the supplemental material, at least for North America (not to mention elsewhere), is not available, that is somewhat understandable. What makes things even funnier about Noike, is that she is both a false suitor, and later on the only one of Tenchi's suitors who has a legitimate claim.
Nachi from Mugen Densetsu Takamagahara Dream Saga has a bit of this; she's also transsexual, and therefore has more fuel for jokes at her expense.
And while that may be closer to Anno's original vision for Rei than is the Moe icon whom the fans have canonized, there is no excuse whatsoever for turning Maya, of all people, into a secretly evil and psychotic member of the SEELE council who implanted Adam's embryo into her hand, just to facilitate Gendo/Ritsuko. Ignoring the fact that this twists Maya beyond all recognition, Gendo/Ritsuko is the one pairing Maya would break up if shewereevil, making this Character DerailmentofCharacter Derailment.
Asuka's counter-argument in many S/R stories is " what the hell does that doll have that I don't?!" To be sure, none of the source material sees Asuka making an eloquent case for pairing herself with Shinji, but give the girl some credit.
Finally, there is more than a hint of Misaimed Fandom in treating this legendary Dysfunction JunctionGenre Deconstruction as a straightforward Harem Anime in the first place. Shinji himself had the choice to turn the show into a harem series in the final episode - and he rejected it as a lie. This suggests that, in the show's own estimate, people who treat it as though it were all about the shipping are even more determined to run away from reality than Shinji himself. Hideaki Anno: even when he's giving his audience exactly what it wants, he's still giving it the middle finger.
And then you have the fans who just dearly dearly want the whole Oblivious to Love and Cannot Spit It Out thing to resolve in canon, and hence will kill off an entire pair just so that their preferred canon pairing can get together faster. That or they just shove their preferred canon pairing into a room and dwell on what happens afterward.
Back in the days of the Digimon fandom, just about every single character had a squad of people out to get them for getting in the way of this or that pairing, most of which would never even happen, and even if it did, many of these victims would have no interest in breaking it up. The main triangles, though, were Takeru-Hikari-Daisuke and Taichi-Sora-Yamato, one a very frequent Ship Tease and the other involving an Official Couple. And before you ask, no, there was no specific popular combination of happy couple and evil rival; the combinations in each triangle were pretty much of equal frequency. Yes, counting the yaoioptions.
In the end Sora and Yamato got together. Which obviously pissed off Taiora fans. As for Daisuke, Takeru, and Hikari? None of them end of with each other but nameless and faceless characters. Pissing off Daikari, Takari, and Daikeru fans alike.
And not even the foreign Digidestined that appeared in maybe two or three episodes are safe from bashing. Catherine, the French blonde girl who helped Takeru and Taichi and got kisses from them in return, is often seen as an horrible threat to Taichi/Sora and/or Takeru/Hikari. In a similar vein Wallace, who kissed Hikari, has got both Takeru/Hikari and Daisuke/Hikari fans out for his blood. Same goes to Rosa, the Mexican little girl infatuated with Ken, who's very much maligned by Daisuke/Ken fans: many after-Grand Finale rants took pot shots at lots of characters, and Rosa was the one-shot female who took the hardest ones (Wormmon didn't like her, so she had to be a little bitch).
Asuka Tenjouin/Alexis Rhodes of Yu-Gi-Oh! GX is not only hated and called all manner of bad names for being the token female love interest and Ms. Fanservice in a show filled past the brink with Ho Yay, but for vehemently refusing to get into a relationship with Manjyome/Chazz.
There's at least one fan that will vilify anyone who so much dares to speak of Judai hooking up with anyone but Asuka, especially if said hook-up is with The Ace Johan/Jesse. With the series over now, it seems they took the best way out and had no ships resolved.
Yubel is frequently bashed and vilified far beyond her actual canon obsessions when it comes to Juudai x Asuka fics. Oddly enough, she doesn't usually get that treatment in Juudai x Johan ones, and it's canon that she's jealous of Johan for having (supposedly) stolen Juudai's love from her.
Tristan/Hiroto, when not paired with Duke/Ryuuji, is usually the Token Homophobe, especially in Joey/Kaiba and Yugi/Anybody. How vocal he is about it tends to depend on the level of Badassedness of the people involved.
In some Kaiba/Shizuka(Serenity) fics, Joey quickly turns Knight's Templar Big Brother when he finds out about their relationship and then cranks it Up to Eleven. This can happen on both sides if Serenity is paired up with Kaiba's little brother, Mokuba, sometimes resulting in Star-Crossed Lovers.
The opposite also happens sometimes in Joey/Kaiba fics, with Serenity being painted as the bitchy, ungrateful little sister who wants to steal her brother's one true love. And for some reason, she's also portrayed as a bitch in Azureshipper (Seto/Anzu) fics out to steal Anzu's true love.
Divine of Yu-Gi-Oh! 5Ds. Go to a horde of Yusei/Aki-fangirls, throw in this name and watch what will happen. It's definitely not fun. Despite him dying twice, which also presumably kills off the possibility of a future development of his romance with Aki in the show, the fans just can't stop bashing him and depict him raping, beating and insulting the living daylights out of her. Usually he dies a terrible death at the end of every single one of their fanfictions. In the show, it was not only made pretty clear that he never would have abused her physically nor verbally, but also shown that even if he used her for her powers, he was in fact always very caring and protective, if not gentle towards her.
Another idea very popular in Yusei/Aki-fanfiction was (and still is) Aki turning against Divine as soon as she finds out about his evil motives and wanting him dead, killing him together with Yusei, or at least being happy about her hero Yusei having slayed him for her. This was completely jossed though in episode 42, when Aki actually did find out the truth and said that even if Divine used her for her powers, she still would always be grateful to him for accepting her and even that his existence was invaluable to her. Also she was pretty happy to see him when he returned in episode 60.
The Jack/Mikage shippers REALLY don't like Carly, and let's not forget how much hate Ushio gets from them.
Although to be fair, since Jack/Carly became far more popular, nowadays Mikage is probably the most hated female character in Yu-Gi-Oh 5d's for still sticking to her admiration for Jack.
Recent episodes show numerous hints of Crow/Aki. Mention this and Yusei/Aki Fans along with the notorious Crow Haters will shout "Crack Pairing" before you know it.
Lately, Sherry LeBlanc fell victim to the Yusei/Aki-fans' bashing as well due to her increased interaction with Yusei and them sharing some pretty ambiguous moments.
In fact, Bruno gets this treatment as well. It's common for Jack as well from those wacky Faithshippers. They just kill everyone off while Yusei and Aki skip through fields of flowers and rainbows. Makes Twilight seem good.
The tiny Hell Teacher Nube fandom really loathes the local Christmas Cake, Ritsuko Takahashi. At first, she's bashed and called "shallow" and a "bitch" for rejecting Nuubee's advances (which were in the Dogged Nice Guy league, so of course Ritsuko would've been weirded out) in a regular basis. And when she does fall for Nuubee after finally seeing his good side, she's bashed and called "third wheel bitch" for threatening the Nuubee/Yukime ship.
Princess Amelia of Slayers is widely hated, especially by fangirls who are Zelgadis/Lina, Zelgadis/Xellos, or Zelgadis/Mary Sue shippers. Generally, the mopey, callous, and bull-headed but still good-hearted Zelgadis would be glorified whereas the naive yet kind-hearted and just Amelia would be turned into an immature, selfish princess with the intelligence of a fish and no fighting skills (she acknowledges her faults in the anime, even!). Zelgadis and Amelia would go up against Zelgadis and Lina (who is an Official Couple with Gourry). Those who do like Gourry/Lina severely tear down Gourry/Sylphiel (the latter having an unrequited crush on the former) and vice versa, citing Lina's sociopathic behavior and extreme selfishness.
Kazumi received a hougu from Pheles in season 2, allowing her to summon Pheles at the cost of her own life. Certain fans think that such a summoning would be a very good idea... Not to mention the reaction by viewers of the second season to her seemingly using that Hougu and fading away...only for the scene to be revealed as one that never actually happened a heartbeat later.
Which is completely stupid, like many other fanfics of this kind, since she poses no threat whatsoever to Shana. Seriously, everyone knows by the end of the first episode that it's a 99% chance that it'll be Shana and Yuuji at the end.It's 100% as of season 3. But if you're watching season 3, you can see that there are.... complications.
Not to mention, the whole fic badly misses the point of the KOR movie it's based on: that it IS possible to re-meet the guy whom you once loved and the friend who got his love... and recover their friendship, thus averting the "rebirth" of a Love Triangle that separated you all.
In Dragon Ball Z... Yamcha often gets twisted into a wife-beater by fans of the Bulma / Vegeta pairing. As long as we're on the subject, why shippers think that a wife-beater would be worse than an Omnicidal Maniac is anyone's guess.
Many Dragon Ball Z fanfics have had Yamcha cheating on Bulma with another woman as the impetus for Bulma to break it off with him and get together with Vegeta, who had pulled a Heel-Face Turn by the time the Frieza saga was over, though he was still something of an arrogant Jerkass. Yamcha being unfaithful to Bulma might have some canon basis, but Bulma wasn't exactly the perfect girlfriend to him either and he definitely wasn't an abusive boyfriend to her at any point. Again, this begs the question of how Yamcha cheating on Bulma is worse than Vegeta nearly letting Bulma and their son get murdered in the Android Saga by Dr. Gero and then Vegeta flat out saying that he doesn't care about them. Surely not caring if your girlfriend and infant son die is worse than cheating on your girlfriend, but not if you follow the shipper's logic.
You also have to consider that there is very limited evidence for Yamcha cheating on Bulma. Future Trunks had a one-liner where mentioned that Bulma dumped Yamcha for being a "playboy". However, Future Trunks is a third-hand source and incredibly biased source as well because he is Bulma and Vegeta's son. (You also have to consider that Yamcha is the guy who used to have panic attacks around attractive women.) We are never actually shown how Bulma and Yamcha ended up breaking up or how Bulma and Vegeta got together. And again, while Yamcha cheating on Bulma would be wrong if that's what happened, Vegeta not caring if Bulma and baby-Trunks got blown up is much worse. (While Vegeta does have some villainous qualities in the android saga, we are sort of supposed to accept him as a member of the Z Fighters and a "good guy" at that point.)
Demonizing Yamcha is even more ridiculous when you consider that Bulma and Vegeta are still together by the end of DBZ and have two children together, so it's not like Yamcha or anyone else for that matter poses a threat to the ship.
It's also interesting and by interesting I mean ridiculous that Yamcha is portrayed as abusive when Bulma is probably more prone to domestic violence. She once slapped Yamcha in Dragon Ball because he had a fanclub and other girls were flirting with him, even though Yamcha never flirted back and generally seemed uncomfortable with the whole thing, and then Bulma told him that she was going to wish for a better boyfriend. Meanwhile, Yamcha tries to make up with Bulma afterwards, even though he technically didn't do anything wrong. Bulma exhibits other controlling behavior in their relationship and has a double standard where it's okay for her to flirt with or eye up other men, but fangirls fawning over Yamcha warrants Bulma flipping out on him and accusing him of being unfaithful. This is in spite of Yamcha seeming to not flirt back with said fangirls and seeming to only care that Bulma likes him. Not saying that we should all write fanfics where [insert character here] rescues Yamcha from a dysfunctional and possibly abusive relationship with Bulma, but the fact is that nearly all the dysfunction in the Bulma/Yamcha relationship was because of Bulma.
There's also the Trunks/Marron (Kuririn and #18's daughter) shippers who bash Pan, and the Trunks/Pan fans who bash Marron, neither of whom have done anything to suggest a romantic rivalry. In fact, Marron doesn't do anything at all. Not to mention Pan and Marron are never shown to be romantically interested in anyone at all, let alone Trunks.
Vegeta is often turned into a wife-beater by Goku/Bulma shippers, and their portrayals of ChiChi, which, while not far off, still make her a victim of Character Exaggeration. Likewise, the portrayals of both ChiChi and Bulma by Vegeta/Goku shippers can get downright ridiculous at times.
Goten/Bra vs. Goten/Marron vs. Goten Palace/Paris/Valese is another popular shipwar. Palace-bashers accuse her of being "retarded" for not knowing how to eat ice cream and make her out to be either a brain-dead valley girl or a conniving witch who wants to ruin Goten's life. Marron is also hated and accused of being a "skank" by her detractors. And Bra wearing a skimpy outfit and being a bit of a primadonna? Must mean she's that mean girl in high school that spread her legs for everyone, if you follow the shipwar logic.
Let's just say that Videl isn't exactly liked by Future!Trunks/Gohan shippers. Or Gohan/Current-Timeline!Trunks shippers. Or really, just expect some Videl-bashing from shippers who pair Gohan up with anyone who isn't Videl.
Piccolo/Gohan shippers either portray Videl as a horrible person or have her be the supportive best friend, depending on how old Gohan is in the fan fic.
There appears to be quite a bit of animosity in the Mai-HiME shipping camp between those deciding whether to pair Natsuki Kuga exclusively with Shizuru Fujino (Natsuki's most important person in HiME and her schoolgirl crush in Otome, a dyed-in-the-wool Schoolgirl/School Supervisor Lesbian with an obvious crush on her) or Nao Yuuki (who teases herlike crazy in Mai-Otome), with fans of one pairing painting the designated "third wheel" as an evil harpy deserving of death (despite both Shizuru and Nao being examples of Draco in Leather Pants).
There's also some Yuuichi bashing by Shizuru/Natsuki shippers, since in the manga, Natsuki's pursuing him, and he's her Key instead of Shizuru (Then again, Yuuichi also gets together with Mai in the manga.
Shizuru/Natsuki fans who follow Otome also don't like Tomoe Marguerite, and make up a large section of her anti-fandom. It doesn't help Tomoe's case that she actually does attempt to hurt/kill people (even going as far as to willingly join the bad guys) so that she can be the only one to get Shizuru's eye/pants... though the kiss was likely the straw that broke the Nanomachine-powered camel's back.
The tagline to the harem anime SHUFFLE is "Which girl would you choose?" Better pick fast, because the Instant Fanclubs depicted in the show have carried over into the fandom, and they're just as crazy as on TV. Kitto Kitto Kaede (pro Kaede Fuyou) and Ai Ai Asa (pro Asa Shigure) in particular have deep, deep vendettas against each other's characters.
This is probably just a symptom of the fact that Code Geass seems to have spawned one of the most bitter and divisive fandoms in recent memory. Absolutely anything seems a good reason for Geass fans to entrench themselves and blame the other side for all the fandom's problems (and for their own bad behavior). So it's not surprising that the shipping is this way too. If you think about it, the shipping is incredibly amusing/distressing when you realise that until Lelouch got, er, "unmasked", not only was the harem ending supported by Divine Right Of Rulership and genetics (Emperor Chuck had 108 wives?), but by two prospective haremettes, the not-entirely-in-the-closet Milly and the unappreciated Kaguya.
If you're a more or less sane fan, do not mention the name Shirley Fenette in front of rabid Lelouch/C.C. or Lelouch/Kallen fans (and even then, it's probably best to isolate Lulu/C.C. and Lulu/Kallen fans from each other for a while). Even after Shirley actually died for the ship.
There's one message board where one poster insists that Shirley is an evil, heartless, manipulative bitch for using her father's death as an "excuse" to get closer to Lelouch, ignoring that she admitted it was selfish and apologized to Lelouch for it, and Lulu reciprocates her feelings to some extent. Interestingly enough, compare the above to the Breaking Speech Mao gives to Shirley in Episode 14 of the first season.
Also, a good part of the hatred that sprung for Rolo comes from people being convinced that he killed Shirley solely out of psychotic love jealousy. Forget that Shirley had the bad luck of saying the wrong thing at the worst moment, Rolo killed Lulu's ONE TWU WUB solely to steal Lulu's heart for himself. Since he was a male after Lulu's heart, there's more than a whiff of fandom homophobia implied. Yes, Rolo's own actions are far from blameless, but he's more a complex Jerkass Woobie than the monster some fans like making him out as to prove that Shirley is "more worthy" of Lelouch's love.
Kallen started getting LOTS of hate after she kissed Lelouch in episode 22 of R2. When that happened, cue to lots of fans (and not only Lelouch/C.C. or Suzaku/Lelouch shippers) screaming "Bitch!" "Whore!" "Slut!" "Skank!" "Kallen is not cool anymore because she's acting like a chick, OH NOES!"
Gino gets a bit of this from the Lelouch/Kallen shippers, partially because he doesn't get a real lot of development and while he seems to have a crush on Kallen, we don't really know how she feels about him at the end of series. The fact that Kallen/Gino is a popular Pair the Spares ship for Lelouch/C.C. and Suzaku/Lelouch shippers doesn't help.
It doesn't help that in the manga and some of the "bad" game endings, Sekai is seen as selfish and manipulative, instead of an impulsive and confused teen. What makes it even worse for her is that Kotonoha is genuinely crazy whenever she goes murderous or suicidal (seen by her Dull Eyes of Unhappiness), but in at least two PS2 game endings Sekai looks and acts creepily sane (or atleast somewhat more in control) when she does the same.
Shippers in the Death Note fandom have been known to come to blows over whether Mello should be with Matt or Near, despite the fact that Matt featured in all of ten panels in the manga, and his appearance in the anime was even briefer.
Much loathing is also directed at Misa Amane for "standing in the way" of Light/L, even though Light sees both of them as obstacles on his path to world domination. Not to mention that by the end, all three of them are dead anyway!
And then there's Halle Lidner. Having a Shower Scene in front of Mello and possibly flirting with him a few times? Apparently, canon proof that the lady is a complete tramp and absolutely unworthy of Mello's attention.
At least one infamous Mello/Near shipper along with a small faction of fans were notorious for insisting Near was Mello's one and only and that Matt deserved to be offed just for that. It was a very confusing and baffling debate that ensued.
No matter what your opinion of the Ichigo 100% ending is, you will be despised by an opposing shipping group, despite the fact that it's universally agreed that the lead, Junpei, is a loser. Possible proof that the entire theory about harem leads being losers so the audience can relate to them is true, as much as the fans hate them.
In a Ranka vs. Sheryl debate on a Macross Frontier forum thread, Ranka gets criticized for being a "barely legal loli moeblob", while Sheryl gets flak for her overly flirty attitude and her somewhat selfish, overbearing personality, even if onscreen, when both are not being rivals to each other about Alto, they have somewhat of a Sempai Kohai relationship, and care for each other a lot (which has more than a Les Yay whiff, for some).
The Fan Dumb got to the point where a formerly well-respected member of a non-English speaking forum actually made up supposed facts to make the impression that one of the creators supported Alto/Sheryl over Alto/Ranka. This was generally seen as fact until members of a different forum got suspicious, tracked down the supposed magazine where the information came from and found out that it was all a lie. (A FAQ with a summary of the events can be found here.)
Cowboy Bebop fans love to pair off Spike and Faye. Julia can go die in a fire, according to them. Or better said, she can get shot on a roof top. Well, that was canon, but it certainly didn't help Faye's cause if there was one.
Fushigi Yuugi fans who would have rather seen Miaka Yuuki hook up with Hotohori or Tasuki often bash Tamahome or kill him off in their fics to make either of the former pairings possible. (Oddly enough, fans of the Miaka/Yui pairing have yet to resort to this.)
Alternately, some fics have Miaka conveniently die in childbirth so that Tamahome and [insert male character and/or Mary Sue here] can not only hook up, they'll have a little family when they do.
And Tetsuya, Yui's eventual canon love interest, is sometimes portrayed as abusive or unfaithful so that Yui and Suboshi can get together somehow, although one would think the fact that Suboshi is dead by the time Tetsuya asks Yui out in the end would be the biggest obstacle there.
Three (four if you count Nuriko'sconfusing stance on his sexuality) of the seven warriors of Suzaku are all canonically in love with the female protagonist, who is hated enough as is, and supporters of all of them are at each other's throats. (The guys at least were savvy enough in canon to set petty love rivalries aside and focus on helping Miaka properly become the Suzaku no Miko) There is also Yui, who is either more deserving of Tamahome (who winds up with Miaka in the end) or gravely hated for blaming Miaka for stealing away a man she only knew for several minutes.
There are also numerous fights between pairings among the Seiryuu Warriors. Never EVER mention Soi and Tomo's common feelings for Nakago if you value your own life.
Even the Yuri Genre romantic comedy Strawberry Panic! isn't immune to this. The Shizuma/Nagisa shippers and the Tamao/Nagisa shippers can get quite violent when provoked. There is also a very large body of fans were angry that Yaya didn't get Hikari, and would rather see Amane get Stuffed In The Fridge.
And they were that close from killing Amane off after she fell off her horse...she gets better to the disdain of every Yaya fan out there. Amane just made a lot of enemies in one fell swoop.
The Sorcerer Hunters sidestory novels introduced a character named Enzeru Fish, who fell in love with Tira at first sight. At least one rabid Carrot/Tira fan was not too happy about that◊. Another fan bashed Chocolat for having a crush on Carrot as well.
On the yaoi side of things, Carrot is often demonized into a homophobic Jerkass who would disown Marron for being in love with Gateau. Conversely, Gateau is made into a raping bastard for the sake of Carrot/Marron or Marron/Tira.
In Elfen Lied, Lucy/Kouta fans hate Team MomYuuka with a fiery passion. Even when, well, she's not exactly the biggest threat to their relationship... but the fact that Lucy murdered Kouta's father and sisteris.
A somewhat surprising exception can be found in the Vision of Escaflowne fandom. The one who gets the hardest and cruelest bashing from fangirls for getting in between Van Fanel and Hitomi Kanzaki is... notMerle the Cat Girl. Though fans do complain about Merle, the one hated the most is actually Allen Schezar, the blond-haired bishonen with a convoluted love life prior to meeting Hitomi (don't ask), who is seen as "sexist", "control freak" and "traitor" because he got to kiss Hitomi in front of Van... when the three were in a sort-of weird More Than Mind Control situation enacted by Folken and the twin catgirls and staged by Dornkirk. That was not Allen's fault (and neither Hitomi's, nor Van's), but people still use that scene to woobify Van and bash Allen.
Rurouni Kenshin fandom has the infamous "Kaoru is soooo emotional and sweet and that makes her better for Kenshin than the ice cold Mary SueTomoe" v/s "Kaoru is a stupid, clingy little bitch and Tomoe was a perfect goddess who made Kenshin truly happy" wars. However, said fans forget that Tomoe was dead long before Kaoru came into the picture, which means that neither of them poses any threat to the opposing ship. It's as if the fans refuse to believe that Kenshin can fall in love more than once in his life.
And if we go to Sanosuke / Megumi fans... Argh. Their treatment of Sayo is horrible. Makes even less sense since not only she's an anime-only character, but she dies.
Some Kyon/Yuki and Kyon/Mikuru fans just won't stop overexaggerating Haruhi's childish, sociopathic and impulsive behavior to downright evil and/or psychotic degrees and denying all the Character Development she ultimately got, while turning the "rival" into a victimised Purity Sue to "prove" how more "deserving" she is of Kyon's love. To them, Kyon doesn't care for Haruhi at all and ONLY puts up with her because he's forced to as a member of the SOS Brigade (read: he doesn't want her to re-write reality without knowing it, but would ditch her immediately if he could). Nevermind that Kyon does gently but clearly tell Yuki in the novels that he likes all the craziness Haruhi brings to his life, and that without her, Yuki and Mikuru wouldn't even be there, so it's thanks to "the evil Haruhi" that they even have chances to approach Kyon.
Kyon/Haruhi fans aren't entirely innocent of this either. A number of the more diehard fans seem unable to accept Haruhi's reduced role in the series, and instead paint Mikuru as an evil, Manipulative Bitch who is actively attempting to steal Kyon away from Haruhi. Never mind that she's apparently required to not get into relationships when outside her time frame, which would make her a Celibate Heroine.
To a lesser degree than the others, Haruhi / Mikuru and Kyon/Haruhi. Aside of the already mentioned incidents, Kyon gets bashed by Haruhi/Mikuru shippers for being a threat to both sides of their ship.
And funnily, the Itsuki/Kyon shippers are just bitter about it all: Pages and pages of Itsuki angst, at times turning him into a completepsycho concerning his inability to be with Kyon, especially because of God-Haruhi, though not limited to it (albeit usually inside his head)... Though given his charade...
The fanbase on at least one anime website is bitterly, bitterly divided on their opinion of Meido Siesta's overtures towards Saito in the anime Zero no Tsukaima complete with rabid fannish gibbering for her death. Even though, as of the second season, Saito is married to his "master", Louise, making them a semi-official pairing.
Which is incredibly confusing since Siesta is generally, and consistently, kind and caring towards Saito while Louise has a Hair-Trigger Temper and will beat him into an inch of his life, well after she develops feelings for him.
There's quite a bit of Double Standard there, too. While Louise is flat-chested, moody, tempery and confused about what love and romance are, Siesta is well-endowed, sexy, aware of her good-looks and willing to use them for her own benefit. You know what that means: slut-shaming of Siesta BY THE WAZOO! (Paired with Louise over-glorification because, for lots of people, it's Double Standard: Abuse, Female on Male.)
It goes both ways really, pretty much every fandom that doesn't ship Louise with Saito will paint her as complete Jerkass with zero redeeming qualities that sometimes just abandons him outright for little to no reason; never mind the fact that not only does she deep down really cares for him and actually shows it sometimes, but that she literally can't live without him (something made extremly clear in the novels).
Which doesn't stop her form kicking his ass and abusing him on a daily basis... A sever overdose of Tsundere, that is.
Boys Love version: In Yami No Matsuei, some Muraki / Tsuzuki fans don't see Muraki's repulsive acts of villainy as the main obstacle to get Muraki into Tsuzuki's pants. The "evil pest" is actually Tsuzuki's partner and Muraki's victim, Hisoka Kurosaki, therefore they bash the crap out of Hisoka and gleefully forget how Muraki is not your average Officer and a Gentleman, but a cruel and sadistic mass murderer who wants Tsuzuki not only because he's pretty, but to use his body to revive his evil half-brother Saki... and kill him as revenge for ruining his life.
And if you go read some Tsuzuki/Hisoka fics, you might find hate towards Ill Girl Tsubaki Kakyouin as well.
Even Tsuzuki is not spared by this trope. In some Muraki/Hisoka fics, he's portrayed as a weak, whiny and self-loathing wangst machine who can't properly take care of Hisoka and thus has the latter running to his murderer/rapist.
While Ayaka and Noriko from Gravitation have received their share of bashing, despite Ayaka willingly conceding Yuki to Shuichi and Noriko being Happily Married to a much older man in the manga, the majority of fanfics simply don't bring them up at all. The guys don't get off as easily: either Yuki is an abusive, heartless bastard who sends Shuichi running off into the arms of someone else (usually Hiro), or Tohma is a psycho stalker who gets in the way of Shuichi and Yuki's love. Granted, Yuki isn't the nicest person and Tohma did try to keep Shuichi and Yuki apart at one point, but neither of them is as evil as many fans would like to believe.
Once upon a time, the Cyborg 009 fandom had a buttload of this. Team Mom Francoise/003 was not only seen as "weak" because she didn't always fight, but if you liked your yaoi (even if it didn't involve her being a "threat") it was a sort-of pre-requisite to hate her. And those who shipped her with Joe/009 fought back... by bashing the most obvious "competition", Princess Ixquic and Carl Eckermannalias Sphinx.
While the Ship Wars have calmed down considerably, the Fullmetal Alchemist fandom spent some time being a major headache. The loudest were the Roy/Riza fans, who hated Ed, Havoc, Al, or anyone else who had even the remotest potential to break up their OTP, but every one of the Major Pairings had its rage-filled fans. And God forbid you were one of those who shipped multiple pairings that traded off characters, threesomes, or didn't like shipping at all.
The weird thing is, there really isn't any need to do Die for Our Ship with Roy/Riza because they make such good Ship Mates with Ed/Win and Al/Mei - and in fact, that's the route most of those shippers usually go. It's just that there's always that Vocal Minority...
Winry can count herself lucky, since most of the Roy/Ed fandom doesn't bother to kill her in fanfic but just pairs her off with Al so Ed can go be gay with Roy. They mostly ignore her completely if they ship the brothers together (or with their own alchemist Mary Sue). Riza is also usually spared by Roy/Ed shippers because it's easy to interpret her feelings as one-sided, cast her and Roy as Platonic Life Partners, and/or ship her with Havoc or another lady. That said, Winry- or Riza-hate is still unfortunately common in FMA slash fics involving Ed and/or Roy (who both mostly get shipped with dudes besides their "canon" female love interests).
The first anime also had Ed/Winry vs Ed/Rose (and slight Ed/Noa). Ed/Win and Ed/Rose fans don't have much of a liking toward the rival character - and frequently bashed her or killed her off in their fanfiction - but both seem to dislike Noa (who is already The Scrappy). It doesn't help that Winry has an Identical Grandchild, and Ed is wearing automail, in an OVA; and that Winry most likely has an Identical Stranger in the Alternate Universe.
Winry and Riza are likely spared because they are generally popular characters even for those who aren't into shipping them. Rose is a Base Breaker to begin with - especially in the 2003 anime, the canon where she's important enough to be a "threat" to the other two main Ed ships - which is likely why she's the most popular candidate for Die for Our Ship. She's simply less mentioned now because she had such a smaller role in the manga and second anime continuity (which also has less Break the Cutie in store for her), but when the first anime was still the most well-known work, she was a frequent whipping girl in Roy/Ed and (especially) Ed/Win fics.
In some cases, Ken may be bashed in favor of pairing Jun off with Joe. The second series even had episodes that had Jun seem closer to Joe than Ken, which gave ship tease for the Joe/Jun faction. It became magnified in the Eagle Riders dub, where viewers bashed "Hunter" for being too whiny and emo as a leader and felt there was more evidence for Joe being a love interest for "Kelly". It didn't help that the ship tease and Hunter's whininess were Flanderization of the original points.
This happens quite often to Keiko Yukimura in YuYu Hakusho, as fans either love her and think she's a great match with Yusuke or hate her and usually make her out to be a jealous bitch (or kill her) so that they can pair him with Kuwabara, Kurama, Hiei, or an Original Character. The same thing also happens to Mukuro, Hiei's boss and potential love interest, who is made out to look like a man and be a power-hungry maniac, if she's mentioned at all, in order to facilitate his hooking up with Kurama. Which is a shame, as the two share a sweet, if at the same time somewhat disturbing relationship, especially in the manga.
We can't forget the hate Kuwabara gets for not being a bishie and turning into putty when he's next to Yukina, can we? Yeah, a good part of the hate isn't pairing based, but some Kurama/Yukina fans do have huge hate-ons for Kuwabara, so...
Hiei/Kurama fangirls who were more into the manga than the anime also tende to bash Maya Kitajima (No, notthat one), Kurama's underclassman with a crush on him who got roped into his adventures once. Nevermind that he erased her memories of him so she wouldn't be in danger again, the fact that Maya got a tiny bit of Ship Tease with Kurama made her an horrid bitch to Hiei/Kurama rabid fans.
This happens to just about every female Weiß Kreuz character who's shown some kind of romantic interest in any of the eight main characters. Ouka Sakaki probably comes off worst; despite the fact that she is both Omi's cousin and dead, fanficcers are still capable of transforming her into an arrogant, shallow Rich Bitch who Omi only dated because he was too polite to tell her where to go. In fact, though none of the four Hitman with a Heart regulars' love affairs last more than a few episodes and Aya's feelings for Sakura were no more than platonic, their would-be love interests are far too frequently bashed for getting in the way of the Ho Yay or a Mary Sue, with Youji's ex-girlfriend Asuka, who was dead before the series even began, being about the only exception.
Even in Asuka's case, some shippers (the ones who don't make her into a Possession Sue, that is) have suggested Youji only hung around with her in the first place in an attempt to prove he wasn't gay, or they sub in a Mary Sue to serve as his childhood sweetheart in her place.
All of this is made especially silly by the fact that canon depicts all of the main characters, especially the four protagonists, as terminal Doom Magnets who are almost guaranteed to get a bridge dropped on anyone who gets too close to them.
This trope often gets applied to Ken for no reason other than his closefriendship with Youji would make Youji's new love look less important. When he's not being ignored completely as a result he's written as a clueless moron, the token misogynist homophobe, jealously and obsessively in love with Aya who never so much as glances in his direction, or any combination of the above.
And then Youji gets amnesia after all the shit that happened to him in Gluhen, gets married to an Hospital Hottie named Asuka Itou and by all accounts lives happily ever after with the girl. You can probably imagine how well the shippers took this. About the only positive is that Asuka Itou usually gets ignored or railroaded into deciding (with ridiculous suddenness) that she wants her beloved to be happy rather than suffering the wholesale character assassination most of the other women face.
Should Amu end up with Ikuto or Tadase? Dare you even mention Kukai? It appears that Ikuto/Amu is the runaway winner, with 90% of the fandom touting it as the deepest, greatest love story ever told and calling Tadase a homosexual (at best) and potentially evil (at worst).
You forgot Kairi, who canonically admited to having feelings for Amu. Oddly, he rarely seems to suffer from Die for Our Ship, unlike Amu's other admirers. This is probably because he was Put on a Bus in the middle of the series.
Naru Narusegawa of Love Hina is demonized by fans of Keitaro/Mutsumi, Keitaro/Shinobu, etc. On the other hand, some Keitarou/Naru fans bash Motoko and demonize her behavior towards Keitarou, while failing to acknowledge that Naru can be just as bad when at her worst. In fact, the whole Love Hina example that used to be here actually fell victim to Ship-to-Ship Combat mentality and had to go, unintentionally making it a great proof of the trope.
The Konami (Konata/Kagami) fanboys can be so rabid, they have been known in the past to bash Miyuki just for the act of being on screen for a few moments. If these fans were the majority, chances are that Miyuki would really die for their ship. It's perhaps a telling sign of the temptations of shipping and Fan Dumbness that an anime satirizing anime tropes and conventions should itself suffer from shipwars.
An alternate-universe OVA series for Da Capo, in which the fan-preferred Kotori wins, was released several years after the original series. In this series, Die for Our Ship is actually invoked: Nemu is shown to have died some time before the story begins. A number of fans were... quite happy about this.
Probably the current #1 cause of dislike for Kaaya from The Tower of Druaga, with many fans believing that Jil had more chemistry with Fatina than he ever had with Kaaya.
Since a sizable chunk of the readership is into Xxx HO Li C for the Ho Yay between Watanuki and Domeki, Himawari, Watanuki's canonLove Interest, has certainly gotten her share of hate. Remarkably not everyone hates her, but if it's not hate, they tend to pretend she doesn't exist at all, or that she doesn't count as a true love interest despite the fact she and Watanuki have actually said they love each other (most try to argue that 'it's just platonic'). It helps that she's seemingly into the said Ho Yay, too.
Worth noting though, certain shippers actually like the idea of Doumeki's Ho Yay with Watanuki being one-sided. It's not so much that they like Watanuki/Himawari as that, in that way, Watanuki is completely clueless to Doumeki's feelings for him.
Things got weird in this fandom when Watanuki took over and confined himself to the wish shop. The result was Watanuki and Himawari (not very willingly, mind you) grew apart, but rather than him turning to Doumeki like many fans wanted, Watanuki instead started pining after Yuuko after her sudden passing away. By this point, Yuuko was already so well-loved that no one could really turn their hate towards her not to mention her being dead meant a) people didn't really consider her a threat and b) she had no control over Watanuki's actions, and some instead started letting their frustrations out on Watanuki himself for being "such a moron" and basically not allowing their ship to come to fulfillment. To make things worse, the Ship Teasing with Doumeki didn't really stop either, which only made the Doumeki/Watanuki fangirls VERY bitter when, ultimately, their relationship remained one-sided to the very end.
Actually, most fans were *ahem*... dissatisfied with theseries'ending... in major part because virtually every ship with some form of fan following got unceremoniously sunk to a certain degree.
Although as of the sequel starting, for now it seems like every ship has yet another chance given that things look to have gone back to how they were before Yuuko's death. Although, considering this is CLAMP, and there are some red flags that something's amiss, one must be wary that things are almost certainly not as they seem.
Lupin III fandom is small enough — and the Estrogen Brigade portion of it especially so — that people don't actively flame one another, for the most part. The Lupin/Jigen, Jigen/Goemon, Lupin/Goemon and Lupin/Zenigata shippers can often hold quite civil and mature conversations with one another. What they will not tolerate is Lupin/Fujiko. Or Anyone/Fujiko, for that matter. Granted, she's devious as a cat and twice as manipulative, but you'd be hard pressed to find any named character on the show who isn't. The Lupin fangirls hate her because she's "mean" to their cute little thief (who harasses every attractive woman he meets, including her); the Goemon fangirls don't care for her 'cause she seduced then dumped their man in the first season (the only really justified complaint on this list); the Jigen fangirls agree with their adorably scruffy gunman, that she's "trouble" (again, take look at theothers' track records); and the Zenigata fangirls (yep, they exist) just think she's a vapid bimbo (who is capable of building an explosive device powerful enough to destroy a solid oak doorbut small enough to fit inside a high heel. This isn't even taking into account the number of times she's saved her male compatriots' necks by charming her way into serving as The Mole when needed. Or the number of times she's freaked out at the thought of Lupin being in peril).
Full Metal Panic!: Gauron/Sōsuke shippers really don't like Kaname. Especially noticeable after the actions of Kaname in the later novels, where quite a few fans Abandoned Ship and actually came to the conclusion that Sōsuke would have been better off continuing with being the emotionless, Assassin Saint Kashim and ending up with Gauron. In fact, there are actually numerous fans of the pairing that feel that Gauron loved Sōsuke and understood him more than Kaname. Therefore, they "matched together better." This is, of course, ignoring all the incredibly creepy and disturbing things that Gauron did, such as being a pedophile molester that desired and obsessed over Sōsuke since the latter was twelve, killed (or attempted to) all of Sosuke's friends / love interests, laid waste to an entire city just so he could get off on seeing Sōsuke's depressed face one last time, and fantasizing about raping Sōsuke's corpse.
Any guesses as to why Nagisa Furukawa is nicknamed "Miss Cockroach"? A part of it comes from her Hair Antennae. The rest... well, ask more than one Tomoya/(read: Tomoyo, Kyou, Ryou, Kotomi) shipper.
Kaorin from Azumanga Daioh is often portrayed as an evil, scheming Yandere bitch who will try to steal Sakaki away from Chiyo-chan... or Tomo, or Osaka, or whoever the preferred partner is.
Crazy as it might sound, a fair number of Zoro/Robin fans seem bitter towards Franky and tend to dismiss or bash him as immature and weird, which probably stems from how he's had a lot more meaningful interaction/character development with Robin than Zoro despite being on the same side for a shorter period of time. That's all. Seriously.
And some Zoro/Nami fans have taken to bashing Tashigi due to being threatened by her possibly showing small hints that she might like Zoro and says she should inexplicably end up with Smoker instead. Painfully brainless when you consider it was never Tashigi's goal to be anyone's woman, and that she doesn't even NEED to end up with anyone at all (which leads to some Unfortunate Implications about what these fans seem to think the role of female characters as a whole should be.)
Let's take special note of the enmity growing between the Luffy/Hancock and Luffy/Nami fans. Dear shippers: Luffy values people period. He'd probably think you were a loser if you hated on either Hancock or Nami. Please reread the damn story to appreciate the fact it's mostly about camaraderie and these things aren't worth dwelling upon seriously. Thank you.
The cast of Ouran High School Host Club have all fallen victim to this. Because you can rationalise pretty much any pairing with Haruhi, fanfic writers will portray any characters percieved as being in the way as evil, controlling, abusive, and the like, particularly Hikaru in Kaoru/Haruhi and vice-versa, or Mori in Honi/Haruhi, and often Tamaki in anything. Because Ho Yay can also be seen in any way you want, there's always at least one victim, usually Haruhi or that character's Heterosexual Life Partner.
The biggest victims are Tamaki's arranged fiancče Eclaire from the anime and Reiko the Perky Goth from the manga, loathed by Tamaki/Haruhi and Hunny/Mori shippers respectively. In Eclaire's case not even her ultimate I Want My Beloved to Be Happy saved her from the fangirl loathing, and in the second it's made worse by Hunny marrying Reiko in the end, sending the Hunny/Mori fans in utter hategasms.
There are two reasons why Lynn Minmay is hated. One is her being an Idol Singer. The other is this trope, because how dare she like Hikaru when Misa likes him too. The one thing that makes this iron-clad Fan Dumb is the fact that Hikaru DOES hook up with Misa at the end, when Minmay rather graciously gives up on Hikaru and decides to stay friends with them.
From No Bra: Mizuki, that skank. Also, some people would like nothing more than to see Masato pushed out of the picture so that Yuki and Kaoru can hook up after reading about some certain revelations about the true identity of "Maa-kun" in canon.
And of course the fans who hate anyone who could possibly endanger the Masato/Yuki ship.
Additionally, several Utena/Anthy shippers hiss at Touga for being a sluttySmug Snake of a Manipulative Bastard, and at Saionji too for being an abusiveJerkass. While it's true that both those guys are terrible pricks in canon, it still doesn't excuse how some fic writers turn them into cardboard monsters whose sole reason for existence is to make Anthy and Utena miserable for the sake of giving the girls extra woobie points.
The pairing of Juri/Miki has recently come under mass fire simply for being heterosexual. Many Juri fans on Tumblr have cried "queer erasure" despite Word of God never having stated that Juri is entirely lesbian, and many fans considering her along with the rest of the cast bisexual.
Hellsing fandom is guilty of this, too. The most glaring example is the hatred against Integra in Alucard/Seras stories. One has her killing herself out of a broken heart. Others have her Seras almost murdering her with a plastic bag. Another has Alucard telling Seras to kill her. Seras's canon love interest, Pip Bernadotte? Doesn't seem to exist in manga based fics.
Ah, Detective Conan fans. Some Shinichi/Conan x Haibara fans seems to really have this mentality going on in regards to Ran Mouri, huh? Ironically, the Shinichi x Heiji fans aren't as hateful towards her.
The Detective Conan yaoi fandom's peaceful in general, especially when compared to the het shippers. Try starting a poll on ANY Detective Conan forum of ANY language debating which female character is their favorite, let alone choosing between Haibara and Ran. Within a couple of pages, it becomes a ballot-stuffing match between Shinichi/Conan x Ai and Shinichi/Conan x Ran shippers, arguing that Ran is a whiny, chickifiedExtreme Doormat that can't think for herself without Shinichi or how Haibara is just a wangstySympathetic Sue with only a few interchangable emotions. The Shinichi/Conan x Ai and Shinichi/Conan x Ran shippers are (depending on the forum) either kept to their own separate threads or couple discussion is banned completely.
On the other hand, as a result, all female character polls would just not have Ai and Ran (In alphabetical order) in the options, calling them "minor female character polls."
In the Higurashi fandom it's best not to mention Keiichi/Rena or Keiichi/Mion outside of fanart, AMVs (obviously not in comments, though) and fanfiction. Any other pairing is surprisingly out of shipping wars though, even ones relating to Keiichi (probably because they're considered not canon). Considering the series, within fan-creations the opposing characters typically do die.
Shaman King gets loads of Ship-to-Ship Combat, and to list all of them would take up several pages of text (and it did). Many Yoh/Tamao and Yoh/any guy shippers bash Yoh's childhood fiancee Anna, and a couple of Yoh/Anna shippers bash Tamao because of her one-sided crush on Yoh. Additionally, rabid RenHoro shippers hate Kokoro for apparently sinking their ship when it was revealed that she's actually the spirit of Horohoro's first love and Jeanne for ending up as Ren's wife or girlfriend, or at very least as the mother of his child.
Hayate the Combat Butler: Ironically for a series where pretty much all the contenders in the respective Unwanted Harems of Hayate and Wataru are remarkably civil toward each other, the shippings fandom tends to be given to bashing the competition. Especially prevalent now with the introduction of the wildly popular first girlfriend of Hayate, Athena, coupled with the series cranking up the Ship TeaseUp to Eleven. The end of Chapter 265 really threw the Hayate x Athena fans into a frenzy when Athena pulls an I Want My Beloved to Be Happy and decides to leave Hayate with his happy life under Nagi, with some Ship Tease of Hayate/Nagi in the last page. Cue some fans threatening to stop reading the manga or that Nagi isn't good enough for Hayate. And this is forgetting that Athena and Nagi, despite not meeting each other, would probably get along well: Nagi gave up her entire inheritance to enable Hayate to rescue Athena without the baggage of a Sadistic Choice and she has shown that, while she may be jealous of other girls with interest in Hayate, she can consider them good friends — like she does with Nishizawa. On the other hand, Athena has expressed admiration for Nagi's sacrifice as well as approval of Nagi for giving Hayate a life where he could be happy.
It is bit jarring since it's been shown time and time again that Hayate doesn't have any attraction for Nagi at all, viewing her as just a little kid. While it is outright stated that she is the person he wants to protect the most, it's more of a Big Brother Instinct.
On the other hand, shippers of all kinds (not only the Hayate x Nagi faction) pretty much started screaming the moment Athena entered into the picture, greatly increasing the Ship-to-Ship Combat since according to them, Athena had to be a stupid and evil Yandere who completely ruined Hayate's life. Yep, her Hidden Depths came after a while, but sheeesh.
Now that Nagi and Athena have met, Athena does throw something of a challenge toward an oblivious Nagi. However, said challenge is mostly of the playful, friendly competition type and displays nowhere near the vitriol (heck, no vitriol at all, for that matter) the more extreme fans of either side purport. So, again, the characters of the manga prove to be much more mature about the whole thing than their shippers.
Tensions were beginning to peak in the fandom's hate of Haruna in To Love-Ru for getting in the way of other ships, notably Rito/Lala and Rito/Yui. The manga was cut short before the hate could truly begin to show, but it was most definitely bubbling under the surface and getting worse. Doesn't help that Haruna was ostensibly based on illustrator Kentarou Yabuki's wife before he found out she was cheating on him and the subsequent messy divorce which cut the manga short in the first place, even when that's not Haruna's fault.
Ill Boy Takaaki in Demashita! Powerpuff Girls Z took quite the heat from Bubbles/Boomer shippers, not to mention the general Powerpuffs/Rowdyruffs shippers who migrated to the series in hopes that the girls would hook up with their evil counterparts. Any other male that the Powerpuffs showed interest in also got skewered hard, as they weren't as "edgy or interesting" as the Rowdyruff Boys. That is, the same Rowdyruff boys who were barely major villains to begin with and only appeared in two episodes of this adaptation.
In NANA, while it is true that Sachikodid get in between Hachi and her boyfriend, it still sucks that she's the one who gets almost all the shit. Same can be said for Reira and Yuri in later chapters.
A few Lotor/Allura shippers in the Voltron fandom demonize heroic Keith into a boorish bastard who just wants Allura for sex, or a crazed Stalker with a Crush who would sooner kill her than let her be with anyone else.
Riho Yamazaki of Night Walker is assaulted on all sides by Shido/Cain and Shido/Yayoi shippers.
Durarara!! is starting to get some of this, among Shizuo/Vorona and Shizuo/Izaya fangirls. Damn Ship-to-Ship Combat! Just from the few stories written about either pairing, Vorona is portrayed as a selfish slut that doesn't care for Shizuo and wants to lure him into false security so she can kill him. As for Izaya, while not bashed outright, he goes through Badass Decay and is defeated by Vorona in a one on one combat easily so she could end up with Shizuo. Fans are forgetting that Izaya is the only character besides Simon that can fight Shizuo one on one when Vorona clearly ran away the first time she came in contact with Shizuo.
Kida's girlfriend Saki Miyajima has recently been getting the same treatment from Izaya/Kida (or anyone with Kida) fans. Most of the time, she's portrayed as a leech that is zapping the life out of Kida or a useless slut that can't do anything and clings to Kida to make her pain go away. Bonus points if this is the reason that the two break up in the story.
The A Certain Magical Index fandom is certainly a clear example, the main Ship-to-Ship Combat is shown between Index and Misaka Mikoto, with the later fandom willing Index to die since Touma spends most of his time cohabitating with her, who lives in the same room on his bed and most of the Accidental Pervert moments are related to her with Touma. Of course this isn't where the hatred ends after reading a while the most common "arguments" to justify their flawed reasons are: "She is a nun" (when in this series is clear that Nuns Are Mikos and despite she is supposed to be at training never acts as one); "She is more like a little sister for him" (Touma oftenly gets embarrased for her on most of his Accidental Pervert moments and that he is always afraid that Index will leave him if she manages to know he actually lost his memories).
In Mirai Nikki, Yuno Gasai loves Yukiteru "Yukki" Amano. Then, Akise Aru also falls for Yukiteru. Yukiteru's feelings are more directed to Yuno than Akise, who happens to be male like him, and Yuno is the most popular character of the series due to her strong feelings, her fighting skills and her physical beauty. Guess what, Akise is loathed by the fandom, and Yuno/Yukki fans even cheered when Yuno killed him.
It goes both ways, actually. The Akise/Yukki shippers hate Yuno for the reasons mentioned above and claim that Yukki being with Akise is a much healthier relationship than with Yuno. This is backed up by Akise getting killed and proving that Yuno plans on killing him just to start the whole game over. Fortunately, this Ship-to-Ship Combat only shows up in relatively few fandom circles.
Puella Magi Madoka Magica: After episode 7, Hitomi Shizuki started to get LOTS of hate for confronting Sayaka on her feelings for Kamijou, and confessing to him a little later. Which, unbeknownst to Kamijou and Hitomi, kickstarts an already VERY unstable and traumatized Sayaka's fall into despairthat ultimately led her to become a witch. She had no idea that such actions would bring that horrible mess, never finds out what's going on and is said to fall into depression when Sayaka's lifeless body is found, but since a part of the fandom seems to believe that Sayaka's healing of Kamijou's arm apparently means she's "his owner" and that he is required to become her prize-boyfriend, the girl is "a traitor bitch who is completely to blame for our Woobie's suffer for stealing her man away". Which brings MASSIVE Unfortunate Implications since it invokes the idea that a woman's worth as a whole person is bound to acting selflessly to the point of being a Love Martyr in regards to a Love Triangle; since Hitomi defies these harmful ideas and refuses to give up on her own happiness when Sayaka doesn't take her chance to ask Kamijou out, she is to be hated and slutshamed and blamed for everything that went wrong.
Interestingly, they seem to hate Kamijou too, with most preferring to see Sayaka hook up with Kyoko Sakura, who only Takes A Level In Kindness while Sayaka is obviously going crazy... which happens after Kamijou doesn't notice her feelings.. Not to mention the fact that Mami specifically warned Sayaka against healing Kamijou's arm to make him "owe" her.
Yuri fans aren't much better, since in some circles, Mami takes lots of heat from Homura / Madoka fans. While this has been around almost from the beginning, it has been specially hard after Episode 10's revelation about the Mami from the third timeline crossing the Despair Event Horizon and trying to kill everyone to spare them from becoming witches, which apparently means she's a "psychotic" and "weak" bitch and "inferior" to Homura. ** It's also extremely annoying to see Homura/Madoka fans compare Sayaka unfavorably to Homura and say that because Sayaka fell into despair for, among many other things, a male like Kamijou whereas Homura became a hardened shell of her old self almost exclusively for a female like Madoka, the first is "shallow", "offensive" and "slutty" while the second is "a beautiful and feminist woman in love". WhattheHELL?!
Some of the Kyouko/Mami shippers are rather disgruntled towards Sayaka to the point of bashing her for being a "whiny, overly emotional trainwreck who doesn't deserve Kyouko's kindness." The results aren't pretty.
While the Soul Eater fandom isn't as loud with this as most other series, it still has its share. There are few cases that whenever a shipper pairs Maka up with other characters-Kid, Chrona, or even Asura- it seems that they find the need to give Soul hell. Some fans have Soul being an abusive boyfriend, a cheater, or just the Jerkass that they see him as- even though it is clearer than anything else that Soul is more devoted to Maka than most other characters could ever be and that the last thing he would ever do to her is leave her.
The Bubblegum Crisis Tokyo 2040 fandom really likes their Linna x Priss Les Yay. It'd be better if they didn't bash the everloving crap of the closest that Priss has to a male love interest, Leon McNichol. He's not an idiot, he's not pure Dumb Muscle, and damn it Priss does develop a soft spot for him and all, so he cannot be as "horrible" and "stupid" as Yuri Fans paint him.
Eleanor Campbell from Victorian Romance Emma. Is it her fault that William Jones and Emma are in love, or that her Jerkass father the Viscount is pressuring her into marrying William to save their wealth? Nope. She's not as hated as other people here, but she still gets pot shots from time to time.
Yoshiki from Venus Versus Virus gets a hand full of this; he's the boyfriend of the protagonist, Sumire. It makes sense, since he's the love interest of the protagonist in a Girls Love series. It helps that he turns out to be a villain in the manga and anime, especially the manga.
Yasuna from Kashimashi: Girl Meets Girl is generally disliked by the fandom. She's the love interest of Hazumu for most of the series, and gets the most attention from her. She's a passive girl who Hazumu deeply cares about, but the most popular couple is Tomari and Hazumu. It helps that in the, more popular, anime she has different characterization and takes things the wrong way causing an Ass Pull.
In the No. 6 fandom, Safu is rather hated for supposedly getting in the way of Shion/Nezumi — despite the fact that Shion/Nezumi is the Official Couple and Safu's romantic feelings are unrequieted.
Shannon in Umineko no Naku Koro ni, for getting in the way of Battler and Beatrice's true love. Nevermind that Shannon IS Beatrice in the first place. Sort of. It's very complicated.
Though relatively new the KyoheixHibino shippers of Kamisama Dolls can be excruciatingly vile. Don't believe it? Check out the comments for episode 11 from Crunchy Roll's stream, despite the fact that it is an From Bad to WorseFlash Back featuring Kyohei, Aki and Mahiru taking on a Powered by a Forsaken Child Kakashi that is seeking one of them to be its next battery, barely surviving the encounter and doing permanent damage to each of their psyche's the most common comments were about Mahiru interfering with their ship, calls for her head and a desire for her to Get a Life...
The Mawaru-Penguindrum fandom is showing baby symptoms of this, as a side-effect of the Ship-to-Ship Combat among Himari/Kanba and Shouma/Himari fans. Shouma is the one that is starting to take the worst, specially after episodes 19 and 20 reveal him as Himari's soulmate - which has sent a good part of the Himari/Kanba fringe into huge hategasms, as they think he's "a pansy" and "less worthy" of Himari than Kanba.
Lisanna Strauss gets this a lot from militant Natsu/Lucy fans, especially after it was revealed that she actually isn't dead and is now back with the main cast, very often being portrayed as the epitome of Ron the Death Eater to justify everyone suddenly hating her and deciding she needs to die. This is completely ignoring her canon personality of being an absolute sweetheart, and the fact that she has actually instructed Lucy to stick close to Natsu as well. This may be due in part to the anime, which added a lot of Ship Tease to Natsu and Lisanna's relationship as children. In the manga, the only hint of romance between them came from Lisanna jokingly asking if she could become his wife when they grew up.
Lucy herself is never killed off by Lisanna fans. It's much more convenient for them to claim Lucy was just a replacement for Lisanna all this time and have Fairy Tail kick her to the curb or otherwise ignore her and drive her to leaving the guild once Lisanna returns. This is helped by a Filler scene added to the anime that suggested Lucy was a lot like Lisanna and that Natsu, who in other filler scenes is shown to be really attached to Lisanna, may have been drawn to her because of that (whereas the manga only has Lisanna tease Natsu a bit when they're really young and Gildarts jabbing at him when he comes back from a job, and no comparison between her and Lucy ever).
Juvia Loxar, while she's a generally popular character and doesn't get as much pairing-related heat as Lisanna, does get some flack for liking/being in love with Gray. Canonically, while she is a Clingy Jealous Girl around him and people (read: women and oddly, Lyon) close to him, all in all, she's a sweet and caring person. Also, most, if not all of her antics concerning him, are pure comic relief, and later on in the manga, she does tone down her obsessive behavior. But that doesn't matter to some non-Gray/Juvia shippers (mostly Gray/Lucy fans) along with the facts Juvia is actually friends with other women (including the ones she thinks are her "love rivals", such as Lucy) and does care for the guild and all its members. They just zero in on her obsessive part of her personality, and slam her for being a total creepy bitch who won't ask Gray out like a normal person (completely ignoring how she attempted to hang out him with a couple of times after she joined Fairy Tail and asked him out to lunch) and needs to die. Or get together with Lyon Bastia since Sherry is (conveniently and blessedly) out of the picture.
On the subject of Juvia, almost all Lyon/Juvia fics paint Gray as neglectful or abusive. There are plenty of other girls in the guild he has good relationships with (Lucy, Erza, and Cana stand out), and really, is it that hard to have Gray let poor Juvia down gently?
On the flip-side, some Gray/Juvia fans paint Lyon as an obsessive stalker who just wants to steal Juvia away from Gray. Granted, Lyon's personality did deteriorate quite a bit after he developed his crush on her, but he eventually pulls an I Want My Beloved to Be Happy and stops pursuing Juvia after he sees that she cares too much about Gray to ever leave him.
Natsu himself sometimes takes some hate from Gray/Lucy and Loke/Lucy fans.
Not quite as numerous any longer, but for a while it was fairly common for Gajeel/Levy shippers to bash Jet and Droy in their fics. Jet and Droy have monster crushes on Levy, who rejected both of them and sees them only as her two best friends and teammates. In fact, they do react badly to Gajeel joining Fairy Tail - but only because the first time they met him, he brutally beat the hell out of them and Levy. They become friendlier to him after he saves Levy's life, but apparently some fans missed this.
Jellal is something of a Base Breaker to begin with, but he gets a lot of crap from some Natsu/Erza fans, who like to ignore the tiny little detail that all the horrible stuff he did in the beginning was while he was under the influence of brainwashing and possession by an evil spirit after being horrifically tortured.
Within the Berserk fandom, there is a radical minority of fans who never seem to give Casca, the female lead of the story, a break. They either hate her because they claim that she's less of an Action Girl after becoming Guts' officialLove Interest, or because she's not with Griffith, OR because she's getting in the way of Guts being with Griffith. Pay close attention to her relationship with Griffith, as some fans are so steadfast at making them the One True Pairing to disturbing degrees, the highest degree which would involve downplaying the fact that Griffith sold out his friends to become a demon lord and as his very FIRST action upon become one, he horrifically rapes her to a very sadistic degree in front of Guts out of spite, which proves to rob her of her personhood, her sanity, nearly three years of her life, and to top it off, her unborn child. It's taken up a notch when some fans argue that she enjoyed being raped. Still, some are confident that Casca well regain her senses - meaning that she will realize that she's in love with Griffith, not Guts. And if Casca can't be with Griffith upon getting cured of her insanity? Well, she's of no use then.
And of course, concerning the GutsxGriffith shippers... Casca is definitely not in the picture here.
You know CLAMP School Detectives fans are way too invested in Ho Yay shipping (even for isCLAMP fandom standards) when they pour hatred on a kindergarten girl like Nagisa because Suoh likes her romantically when he could be more invested in Nokoru. Her best friend Utako manages to mostly dodge hate, but mostly because she's paired up with Akira in canon and thus she takes him outta the picture.
Sakamichi No Apollon is starting to get this. Because how dares Ritsuko be a cute girl and catch Kaoru's romantic attentions when, according to some yaoi fangirls, there's only Ho Yay making out with Sentarou to be done!
In Air Gear, asking who should be Ikki's love interest is like asking for a bloodbath. The sections that support Ringo, those that prefer Simca and the third ones supporting Kururu shall NOT meet each other, lest we'll have massive flame wars. And this doesn't count the Kazu and/or Ak/g/ito fans...
Akito's Clingy Jealous Girl Yayoi Nakayama seems to be the one attracting more hate, though. It got so bad at some point that rabid Akito fangirls actually put up online petitions to try pressuring Oh! Great into killing off Yayoi so Ak/gito would be "free" from her.
Are you into Aquarion EVOL? Please, never ask whether Amata should've chosen Mikono or Zessica. Many Zessica fans (with some of them tending to use her as a Possession Sue) will immediately bash/slutshame Mikono for catching Amata's attention and call Amata an Ungrateful Bastard for rejecting Zessica's love declaration and choosing Mikono over her. In the meantime, Mikono fans will likely retaliate via slutshaming Zessica and calling her "weak" and "shallow" for being overly depressed over Amata's rejection and getting body-jacked by Mykage afterwards.
Don't forget how some Kagura fans are pissed at Amata for being the dude Mikono loves despite also being Kagura's Morality Pet, and thus they also call Amata a tool and an asshole who stole Mikono from Kagura. Because for these fans, the fact that Mikono is the Nice Girl whom Kagura is obsessed with means that Mikono automatically owes Kagura pussy and Amata is a cockblock who steals her away from him, huh?
Miraculously averted (by now) in Kuroko No Basuke's English fandom, where Momoi and Aida (who'd normally get hated and slutshamed to Hell and back) are mostly ignored but safe (and often pairedup). It's actually the Japanese fandom that indulges into this: the most common victims are Kagami for the avid Aomine/Kuroko shippers, and Kuroko for the Kagami/Himuro shippers.
Being a harem series, Sekirei is not immune to this even with strong themes of True Companions and the stated desire of the Marry Them All solution. Musubi gets this for being the primary heroine, an Idiot Hero, and supposedly in the way of whichever member of Minato's harem is preferred. It isn't unusual to find fanfiction where she is killed off, written out of the harem, or completely ignored. The other primary target is Mikogami Hayato, because he is a very real stumbling block to the Fan-Preferred Couple of Minato and Akitsu. Discussion of his impending death and Akitsu running off to join Minato's harem occurs literally every single time a new chapter is released.
However, ever since episode 6 the fandom plays it straight... in regards to Go's brother Rin. After his less-than-graceful reaction to defeating Haruka in a race, the Makoto/Haruka shippers have been screaming for his death. The Rin/Haruka fans have retaliated by accusing Makoto of being boring (at best) or codependent/clingy (at worst)
Gou's school friend Chigusa Hanamura has gotten occasional pot-shots from Makoto/other guys fans after Makoto praised her cute looks once. The fandom has reacted accordingly.
The apparition of Sousuke Yamazaki re-ignited the shipwars, with fans on both the Makoto/Haruka and Rin/Haruka sides shaking and crying at the possible "threat".
There is a rather famous scanlator/translator who has been accused of being extremely biased towards Rin/Haruka and hating the Hell out of Makoto for being "the other woman". i.e., she would intentionally post snippy comments abnout Makoto in the Makoto tag and in his birthday, whine about how codependent he's to Haruka, and then post supposed "translations"of the novelsproving how obsessive he is to make him look bad.
Hamtaro: There are some Hamtaro/Bijou shippers that tend to write fanfictions that portray Boss as the bad guy, and sometimes even make him act very out of character either in a Stalker with a Crush persona, or a Crazy Jealous Guy persona, or a combination of the two based on a kind of Love Makes You Evil way of thinking. While the "real" Boss (i.e. non-fanfiction written) does tend to get jealous at times due to his crush, it's unlikely that it would lead to such a drastic Face-Heel Turn that would make him the unlikable and unsympathetic villain that he becomes in some of these fanfictions.
In Akame Ga Kill, there are quite a few fans who would like Esdese to Murder the HypotenuseMine (which, given the recent events and the Anyone Can Die nature of the story, might actually come to pass) and have Tatsumi all to herself. Keep in mind that, while certainly humanizing, Esdese's love for Tatsumi is still extremely selfish, as she doesn't care about Tatsumi's opinion and want to impose her own feelings upon him. The fact that Mine's crimes amount to being a vigilante who kills despicable criminals, in contrast to the craploads of good people Esdese mercilessly slaughtered, doesn't seem to hinder the Tatsumi/Esdese shippers in any way.