A shipping war has sprung up in Sonic X, centered around Tails/Cosmo vs Tails/Cream. Fans are prepared to kill the characters off to get their ship. In Tails/Cream's case, this isn't necessary; Cosmo died in the last episode. However, Tails/Cosmo fans find ways to return her to life, often via the seed Sonic found. This is illustrated in a somewhat disturbing manner here.
Bakugan is somewhat a curious case, as the main target is not Dan, but Shun, his Lancer and Foil. The first season teased Alice, while third season teased Fabia. Surprisingly, the shipwar is notably low on bashing and cursing, with each side prefering to pile evidence to try and top each other.
In the Mazinger universe fandom you find two kind of people: those that think that Kouji Kabuto was in love with Sayaka Yumi, and those that think that he barely cared for her like a friend (Sayaka has always been his Official Couple or at the very least Implied Love Interest, but you talk about facts to a shipper) and he paid more attention to any other woman that showed up in the series (Misato, Erika, Minerva...). Kouji/Maria are the largest faction of the second group by far, due to the sheer amount of people watched Grendizer first. And then you have the people who ships Sayaka with Boss, or the arguments among Duke/Hikaru and Duke/Rubina shippers. However, debates between shippers are refreshingly civil and without mud-slinging.
What is generally considered the bloodiest ship war ever took place in the Pokémon fandom. The main debate seems to be what combination of the constantly-fluctuating Power Trio should hook up; there's at least thirty possible sides, each with a knife to the throat of the others. Also, there's the Rocketshipping (Jessie/James) debate, although there's no one else to pair them up with - Anti-Rocketshippers simply hold the opinion they're not interested in each other (and usually that James is gay).
The main war was between Pokéshippers (pairing up Ash/Satoshi and Misty/Kasumi) and Palletshippers (Ash/Satoshi and Gary/Shigeru).
Perhaps the fanatical nature of Ship-to-Ship Combat is best exemplified by the fact that the Ship War can be described as HAVING TREATIES and civil wars. There are times to just give up, fanboys AND fangirls.
Considering the core cast contains no less then ten main characters, there are literally dozens of one-season villains and one-shot "best friends", and the two members of the most official couple have five or more suitors apiece—and there are several canons to the series—it's no wonder Sailor Moon is a quagmire of ship related insanity. Specifically, the debates between Mamoru fans and Seiya fans can get really ugly. There's also the Uranus/Neptune shippers versus the "they're just close cousins!" sect... although that one is more a battle against outright lies (example: Prince Uranus) by fans who don't like same sex pairings.
There was also Kurogane/Fay and Chi/Fay, although the latter ship pretty much died out later on.
Magi - Labyrinth of Magic has Sinja (Sinbad x Ja'far) shippers versus Sinju (Sinbad x Judar) shippers. Fanart of Sinbad often features either Ja'far or Judar as his romantic interest. While Sinbad's relationship with Judar is more Foe Yay than Ho Yay as with Ja'far, both ships are more or less equal in power.
There's people out there that would prefer see Morgiana with Hakuryuu rather than Alibaba despite canonical evidence that shows she likes the latter...
Also, if you support Kougyoku's crush on Sinbad, you might be marked for a very painful death.
Ao-Kuro shippers (Aomine x Kuroko) against Kaga-Kuro shippers (Kagami x Kuroko). Aomine and Kagami are very similar in many ways, both being Kuroko's past and present 'Light' respectively. More often than not, Kaga-Kuro fanfic will usually portray Aomine as an antagonist, and vice versa for Ao Kuro fanfics.
Momo-Kuro (Momoi x Kuroko) against Ao-Momoi (Aomine x Momoi). Momoi has a heavy crush on Kuroko since their middle school times, but chose to go with Aomine to Touou high-school to take care of him instead ('childhood friend's duty' as noted by Momoi). This causes fans to argue whether Momoi's feelings for Aomine is purely platonic or not. Plus, Aomine once mentioned that he likes "women with big boobs", which Momoi clearly has. One of the end cards in the anime which showed Momoi lying down with Aomine doesn't help either, it was a blatant Ship Tease by the animators, leading fans to question their relationships even more.
Ao-Momoi vs Ao-Kuro. Moments after the end-card was shown, a fan-edited version replacing Momoi with Kuroko was instantly uploaded to the internet.
Spike/Julia vs. Spike/Faye for Cowboy Bebop. Many Spike/Julia fans insist Faye is a slutty, obnoxious bitch who's too immature and whiny for Spike, while Spike/Faye fans often believe Julia's a fickle syndicate whore who destroyed Spike's relationship with his former best friend and ultimately got him killed.
Yu-Gi-Oh! 5Ds Scoopshippers, take arms! Tonight, the Careshippers come! But THEY ARE NOT PREPARED!
Many Naruto fans enjoy milking the loads of possible combinations within the Five-Man Band for all they're worth.
The Naruto fandom's version is Naruto/Sakura fans versus Naruto/Hinata and Sasuke/Sakura fans. Starting a shipping thread on any of these couples, on any anime/manga message board, is tantamount to throwing a live hand grenade.
Kishimoto himself threw the grenade twice, with Naruto/Hinata in chapter 615 and Naruto/Sakura in chapter 631.
Apparently, a new group is forming that's against all three big and popular ships, mostly out of disgust for the canon portrayals of the relationships and the years-long ship war over them.
That group is composed mainly by Sasuke/Naruto fans (and Sasuke/Karin, so that disgust is as much as pairing wars as the rest of them). The number of neutral parties is actually quite small in comparision.
Even side ships are not safe. Shikamaru/Temari and Shikamaru/Ino wars can pop up at any time. And you're just asking for it if you say Sasuke should end up with Karin and not Sakura or Naruto.
And never, ever get yaoi involved, because then hell really has broken loose. Most yaoi shippers will stay out, but the ones out for more amusement/blood will insert themselves into the argument by saying their ship is better/more canon than the others being "discussed".
Heck, even people on the same side of shipping can be incredibly vicious. Sasuke/Naruto vs. Naruto/Sasuke, anyone? And don't you dare say these are the same pairing deep down. For those of you who are understandably confused, the order apparently indicates who the dominant person in the relationship is...
The flames and the war have turned out pretty nasty after Neji's death and sacrifice for Hinata. There were ugly battles between Neji/Tenten vs. Neji/Hinata vs. Naruto/Hinata fans. Neji/Tenten fans defended their ship by sustaining that Neji's sacrifice for Hinata was only proof of familial love, not romantic, while the Neji/Hinata fans saw it as proof of both familial and romantic (since simple cousins don't usually do that kind of sacrifices for each other), with more on the romantic part (since, in Japan, cousin romances are viewed just like the other romances and since "Naruto" is a Japanese show, anything could have been implied). Heck, even Naruto/Sakura fans decided to throw their two cents in, calling out Hinata for 'selfishly getting Neji killed'. On the other hand, a part of the Naruto/Hinata fans sustained that, even if Neji had that kind of feelings for Hinata, Hinata still didn't care about Neji and still loved Naruto, while another part sustained that Neji actually gave "his blessing" for the Naruto/Hinata ship and, along with his death, he has gotten out of the way. It doesn't matter that none of all those had actually anything to do with the true reasons Neji died for; namely that he, as a man supposedly resigned to a pre-destined fate, was able to 'choose' his destiny, mirroring his father's actions.
Anything involving the Akatsuki, particularly Deidara.
Bleach: The Ship-To-Ship Combat between fans of Ichigo/Orihime versus fans of Ichigo/Rukia is particularly bloody.
Most of the existing Bleach forums out there were established during the Soul Society arc, a period of time when the fandom considered Ichigo/Rukia to be canon and Ichigo/Orihime to be a Crack Pairing. However, as the latter pairing gained development, the forum environments turned hostile (as some moderators were more likely supporters of the former) and wank ensued (possibly causing the downtime of an entire forum during a peak period). To this day, shipping sections on Bleach forums are usually heavily regulated or missing entirely, and the majority of Ichigo/Orihime fans have banded together on their own ship-oriented forum.
Some Ulquiorra/Orihime fans have also joined in the Ship-to-Ship Combat against Ichigo/Orihime. Orihime is frequently criticised for not falling out of love with Ichigo and is blamed for the Break the Cutie events that happen to her — some of them being caused by Ulquiorra. Alternatively, these "special" fans tend to deliberately handwave or completely erase Ulquiorra'slesssavorytraits to make him look like Orihime's "perfect prince" who'll whisk her away from Ichigo... nevermind that the major appeals of the couple would be the potential Mind Game Ship, Angel/Devil Shipping, Corrupt the Cutie and/or Foe Yay aspects.
Some yaoi and Ichigo/Orihime fans have jumped into the Ship-To-Ship Combat by bashing Ulquiorra/Orihime with accounts dedicated to it, and obnoxious stamps. Noting the first reference, it's particularly noticeable how much utter contempt there is for Orihime. She just can't win in fandom.
Black Butler pretty much is a war within itself nowadays, especially with the new season. (What else is expected though, when every male in the show is a total Bishōnen?) Despite the only confirmed canon pairing being the (platonic) love between Sebastian/Any Cat He Can Find and the closest thing Ciel has to a canon "loveinterest" is Lizzie many fangirls persist over pairings like Ciel x Sebastian, which has some Yaoi Fanservice in the manga and was Turned Up to Eleven in the anime (especially in season 2). Though Sebastian's obsession with (eatting) Ciel's Soul may make it somewhat canon in its own right. You'll also stumble along Sebastian paired with Meirin, Finnian, Bard, Alois, Lau, Claude, Tanaka... Try giving a solid standing for your pairing in a ship board, or especially on YouTube, and you'll usually have at least 5 people calling you a bitch. This fandom tends to be nicer, but still.
Aside from the most common pairings of Master/Butler, Ciel/Sebastian and Alois/Claude, the circus arc opened a new possibility of a Heterosexual Pairing with Ciel. You now have the option of supporting Ciel/Lizzy, or Ciel/Doll aka Freckles. You can find a couple forums with wars about this. A lot of it is troll logic about how if Ciel really loved Doll, she'd be in the anime, or if he loved Lizzy, insert whatever reason you like. Oh, and if you think you're safe just sticking to Alois/Ciel, which is practically Belarus/Russia based on certain fansubs, you're not.
Actually, the only pairing that doesn't get too fought over is Lau and RanMao. It's rarely shipped, but no one fights over it. Probably because it's pretty undeniable that it's hot.
Rurouni Kenshin fandom has no shortage of shipping wars to decide who was/would be be better for Kenshin: Kaoru or Tomoe. Though they're usually one-sided: Tomoe wasn't introduced till the final arc of the manga and doesn't even show up in the anime (only the Tsuiokuhen OVA) and is the tiniest bit dead by the time the main story starts. Guess who has the bigger fanbase.
Don't forget Shura, the Pirate Lady Kenshin meets. A smaller fanbase desperately wanted her to be with Kenshin.
Megumi also became quite the victim of ship-based bashing. Kaoru/Kenshin shippers did not take her teasing personality in stride as well as her open interest in Kenshin (which she didn't relinquish until the Kyoto arc), and accused her of being a whore who only wanted to get into Kenshin's hakama and hated Kaoru (despite Megumi being a Cool Big Sis to Kaoru and doing what she could to help her when she had an Heroic BSOD). They mellowed out later and started shipping herwithSanosuke instead, and then Tomoe took her place as "Kaoru's love rival".
Very ironically, some rabid Sanosuke/Megumi did NOT take the apparition of Magdaria and the Ship Tease she got with Sanosuke well at all, and even Magaria's death wasn't enough to shut them up. ("Weh weh, the bitch is dead but Sano is so saaaad! Why ddi they create that bitch only to get her killed and make Sano cryyyyy! WAHWAH!")
Digimon fandom suffered from a terminal case of Pair the Spares in its early years that went something like this: "Digidestined must be paired up in descending order by importance." Thus, Taichi/Sora, Mimi with either Koushiro, Yamato, or Jyou (despite that she rarely even speaks to the first two) and Takeru/Hikari. Then Hikari was bumped up to female lead in the next season opposite newcomer Daisuke, and a whole new pairing sprang up. Which wasn't helped at all by the continued and increased Ship Tease of Takeru/Hikari. Then everybody stopped keeping track when the Distant Finale paired Yamato with Sora.
Taichi/Sora and Yamato/Sora fans still have it out once in a while. Taichi/Sora fans rationalize that Yamato comes off as a huge douche for part of the second season and therefore can't stand the thought of him ending up with Sora, or that Taichi and Sora were "obviously" flirting/in love with each other for the entire first season so Sora ending up with Yamato instead was a giant cop-out. Yamato/Sora fans use the Distant Finale, the fact that Sora willingly chose Yamato over Taichi without anyone pressuring her into it (and having her back off could have sexist Unfortunate Implications about her feeling that "she owes Taichi affection"), the other fact that Taichi got over Sora's supposed "friendzoning" in less than 24 hours (and even showed attraction to another girl named Catherine so he wasn't as "hurt" and "spurned" as Taichi/Sora fans insisted he was), and how it breaks the "Hero gests together with Heroine" clichés for rationalization, with some of them pointing out that many people end up with someone other than their oldest friend/first crush. And in the middle, the Taichi/Yamato fans- often considered the most populous shippers in Digimon fandom- are very bitter because of the constant Ship Tease between Taichi/Yamato in the first season, including official Taichi/Yamato art published in a magazine. The whole debate over whether Yamato and Sora were Strangled by the Red String or not will probably never fully die out, in fact.
Not even the Digimon themselves were spared. In most cases, the Digidestined who were paired had their Digimon paired up with each other. The more well-known one is Patamon/Gatomon (or even Angemon/Angewomon), and Veemon/Gatomon. Though this becomes a bit of a shipping three-way battle when Wizardmon/Gatomon gets involved, and they've all butted heads with one another numerous times in the past.
Special mention goes to the war between the Davis/Kari shippers and the TK/Kari shippers. For a short time on Fanfiction.net, a person by the name of Mykan (known for /My Little Unicorn) somehow became leader of a group of Dakari shippers (and thus earning him the name "Dakari-King Mykan") and invoking a flame war that he himself compares to World War II.
"But Master Marik, it is obvious that Yugi is in love with Tea." "What? No way, that's insane! What kind of messed up fanfics have you been reading?"
The Lyrical Nanoha franchise has the battles between the Nanoha/Fate and Nanoha/Yuuno factions, which is not helped by the creators knowing about it and fueling both sides with loads of Ship Tease to keep the flames burning. There even seems to be a division in the lesser ranks of the production themselves; for example the Megami Sound Stages seem to support Nanoha/Yuuno; while the actresses who play Nanoha and Fate are convinced they're a couple. These flames, however, while apparently violent, tend to be pretty friendly overall (perhaps due to the theme of the show itself), and people who take it as Serious Business are routinely mocked in the fandom.
Nanoha/Chrono was a third fleet in the running for a long time, too. You should have seen the looks of disbelief when the authors sank the possibility of Chrono/Nanoha or Chrono/Fate by pairing him up with Amy and making his mother adopt Fate (not that this last one would stop some people, of course). At least the shippers of that have some comfort: it's canon in Triangle Heart 3: Sweet Songs Forever, in which neither Yuuno, Fate nor Amy exist.
Anyone who spends time on the AnimeSuki Forum learns about the historic and brutal 300 vs. LegionFlame War. The supporters of NanoFate shipping called themselves Legion due to their sheer numbers, while YuuNano shippers called themselves 300 since they're so few.
The Tezuka x Fuji pairing is often bashed by fans who ship them with others, specially Fujicest and Atobe x Tezuka fans ( And it's made worse after Fuji and Tezuka DO get Ship Tease in the manga itself — apparently inspited by the anime subtext). Taka x Fuji fans are NOT innocent of this either, as sometimes Taka/Fuji fan corners are made of passive-aggressive jabs about how Tezu/Fuji fans are "only in for the pretty UNLIKE OUR MUCH DEEPER SHIP".
The few Ryoma x Sakuno and An x Momoshiro fans are often automatically accused of being "homophobic" or "having the icky, useless girls take Ryoma away from Momo" by slash shippers... even if these "homophobes" do ship some slash couples alongside the het ones.
The Het is Ew factor gets even worse if you even mention the girls from the Dating Sims. These stupid Mary Sue whores! They "straighten" super gay gay GAY characters with their evil vaginas and steal them from their "more deserving" male lovers, EWWWWWWW!
Inui x Kaidoh fans bash Yanagi and the Inui x Yanagi pairing and fans, accusing Renji of being hateful and cruel towards Inui as well as a bad and abusive friend when they were younger;
Macross Frontier fandom has fighting between those who want Alto to end up with Sheryl Nome (the accomplished star), or with Ranka Lee (the Moe starlet). Naturally, this irks the fans who are in it for the Humongous Mecha, the story or the music, or some combination thereof, as one anonymous 4Chan user put it: "This kind of ship-to-ship combat doesn't belong on /m/!"
More interesting is that while all Macross series have love triangles, this one is especially complicated since there is some subtext between Ranka and Sheryl and even some scenes that can imply a threesome end. So the shipping war is actually between Ranka/Alto, Sheryl/Alto, Sheryl/Ranka and Ranka/Alto/Sheryl.
This is mostly a redux version of the shipwars in the original Macross fandom. Replace "the accomplished star" with "the Broken BirdBridge Bunny" (Misa), and the "moe starlet" with "the Chinese Girl that became a rising Idol Singer" (Minmay) and BRACE YOURSELF for the Hikaru/Misa fans going absolutely BERSERK at the mere mention of Minmay, bashing her and falsely accusing her of being a slut who played with Hikaru's feelings since the beginning (despite how she dealed with problems of her own) and who is oh-so inferior to the Ultra Mature And Powerful Strong Woman Misa (despite Misa being much more complex than that.)
The InuYasha fandom is more or less evenly divided between fans who think that Kagome is an abusive Scrappy whose love for InuYasha isn't nearly as true as that of tragic paragon Kikyo, and fans who think that Kikyo is a psycho ex standing in the way of InuYasha and Kagome's true redeeming love. Never mind that one is the reincarnation of the other, and thus the question is less "who" than it is "when".
Tamao and Yaya didn't have it easy despite a good army of shippers for their side for Strawberry Panic!. While the original vote was open-ended, the anime had the pairings settled as Nagisa with Shizuma and Hikari with Amane. And Tamao doesn't even have another girl to fall back on... talk about fighting for a sinking ship.
Neon Genesis Evangelion is rife with this, though of a more subtle and insidious brand than any of those above. There is great mutual enmity between the Rei/Shinji shippers, and the Asuka/Shinji shippers, which isn't helped by the fact that Asuka and Rei pretty much hate each other in canon. There are also the more controversial Misato/Shinji shippers, the Kaworu/Shinji shippers, and the occasional fans of Mana Kirishima. Thanks to the ambiguity of the series, each shipper has their own personal character interpretation which each defends with fanatical fervor even against others within the same shipping subset.
The fact that there are several Alternate Continuity settings to work with can complicate matters even further.
The Rebuild of Evangelion films have also helped reignite the debate by giving a new continuity to work with. The Ship Tease between Shinji and Rei made many shippers jumping the gun and declaring them Official Couple, whereas Shinji/Asuka supporters argued that Shinji/Asuka got plenty Ship Tease too, and the Rei/Shinji couple was doomed anyway because would inevitably would be revealed that Rei has been built with the DNA of Shinji's mother Yui just like in the original series and that she and Shinji are simply confused about the type of love they have for each other. Finally Evangelion3.0 wrote off Shinji/Rei, and now the fight boils down between the Shinji/Asuka fans and Mari/Asuka shippers, apart from giving the Kaworu/Shinji pairing more ground.
Back in the early days of the Internet, the large and prolific Ranma ½ fanfic community engaged in a huge three-sided shipping war among the partisans of Ranma's three "official" fiancées. The flanderization, mischaracterization, recriminations, demonization, and outright nastiness still echoes through fanon more than a decade later.
It got so silly that people actually accused a group called "The Defenders of the True Fiancée" of spreading viruses and hacking websites. One particularly notorious shipper even accused the animators of conspiring against his favorite character.
Tenchi Muyo! has had several bloody ship wars that have been known to tear apart forum communities. Everyone has their favorite girl. Back in the day the major ship wars were between Tenchi/Ryoko and Tenchi/Ayeka fans, but as of late, Tenchi/Sasami fans have become more vocal. The fact that the series pretty much has a canon Harem Ending has done little to quell the fury of the shippers who think Tenchi should end up with their favorite girl.
For Black Cat, Creed/Train fans and Saya/Train fans don't really get along. Huge arguments were made over whether Train ever liked Saya as more than a friend, which evidently would make it more canonical than the pairing of Creed and Train. Not that any of this really matters, considering that Saya died very early in the story and that Creed is the Big Bad with a rather questionable grip on sanity and whose obvious homolust towards Train is equally obviously one-sided.
Amongst Shugo Chara! fans, there is definitely animosity between the Tadase/Amu and Ikuto/Amu factions, with the expected Die for Our Ship mentalities.
The Konata/Kagami army vs. the smaller but equally hardcore Konata/Miyuki camps in Lucky Star, even though this anime spends much of its time satirizing anime tropes and conventions. Oh, the irony.
Generally, Ai Ai Asa-senpai members are the targets of an Enemy Mine by all the other fanclubs, even going as far as to call Asa a "selfish bitch."
Oddly averted in the Katekyo Hitman Reborn! fandom. Everyone is free to ship whatever they like, and very few people would have a serious debate about it, since most people are multi-shippers. Considering Tsuna and the Loadsand Loadsof Characters, it's not hard to see why. Although there seems to be opposition between Gokudera/Tsuna shippers and Yamamoto/Gokudera shippers.
Higurashi no Naku Koro ni has a somewhat mild case of this. There's Rika/Hanyuu vs Rika/Satoko vs Rika/Keiichi vs Keiichi/Satoko vs Akasaka/Rika. However, the most obvious is Keiichi/Rena vs Keiichi/Mion. For some reason, Keiichi/Rena was more popular in the past, but now Keiichi/Mion is. Same with Rika/Satoko and Rika/Keiichi, that used to be the least popular Rika pairings.
Post-Kai anime OVAs seem to be having a field day with the Rena-Keiichi-Mion love triangle. This has only added fuel to the shipping war flames.
D.Gray-Man: The shipping wars of pairing Allen with their favorite OTP. The sad thing is that he hasn't even really shown that much interest in any of them, being a confirmedCelibate Hero who has expressed adamant disinterest in anything romantic. There's the obvious wars between Lenalee/Allen and Road/Allen fans, and then there's the Ho Yay / Foe Yay shippers (Kanda/Allen, Lavi/Allen, Tyki/Allen)...
With the resolution of the Greece Arc a lot of this has died down, with large parts of the fandom picking sides on the Hinagiku/Hayate/Athena Love Triangle, thanks in part to the reveal that Hina has a past with Athena too, Hayate still had feelings for Athena (which he told Hina no less), but was ultimately rejected before finally revealing that Athena was planning on coming back to Japan after all - even giving Nagi the empty box for the ring Hayate gave her as kids which many saw as a direct challenge.
The flames rose up again with the introduction of Ruka into the mix, some seeing her as a refreshing change of pace with her forwardness while others saw her development as rushed since she didn't take the time to get to know him that the other girls did. Then there was the promise to make him marry her if she won the manga competition with Nagi. That...didn't go over well with many. By now, the forums are still largely Hinagiku vs. Athena (with a small amount opting for the One True Threesome) and the much smaller groups who support him with Nagi or want Ruka to return.
Death Note has a couple pairings, such as Light/L, Mello/Near, and Mello/Matt, along with pairing any of the above with an original character in fanfiction.
There's also a minor shipwar between Light/Misa and L/Misa shippers. Needless to say, neither get on well with the Light/L shippers who were as much of an inspiration for the Het is Ew trope as Heero/Duo. The shipping wars simply tend to be more along het and slash lines rather than within the slash and het fandoms, with Misa and Halle getting bashed because they take Light and Mello away from their potential male partners.
Back in the early years of the Slayers fandom, there were some pretty heated ship wars between Lina/Gourry and Lina/Zel shippers, made even more fun by Lost Universe with shared voice actors and character archetypes, not to mention fanon shared continuity. It's calmed down considerably since.
And then Shinn and Lunamaria's Japanese voice actors got married. I guess that's a solution, too?
Mobile Suit Gundam 00 has seen its share of Ship-To-Ship Combat, with fans endlessly debating about who Setsuna should be paired with, whether it be with Marina Ismail, Feldt Grace or Nena Trinity. It doesn't help that supplementary materials (which incidentally are considered non-canon) released lead to complications as to who Setsuna will really end up with, thus leading to further confusion and debate.
With the announcement of a new Fullmetal Alchemist movie after the series has ended, the new female character is already getting Mary Sue calls and "she better not break up my OTP" shit. We don't know ANYTHING about her, and she's STILL being accused of Suedom? Come ON, Fan Dumb!
Although not as bad as it used to be, the 2003 anime version's fandom fought hard over the classic trio of Ed/Winry, Ed/Rose and Ed/Roy. Poor Rose herself was on the receiving end of Die for Our Ship quite a bit, to the point that even mentioning her name on a Ed/Winry forum is...discouraged. (Winry and Roy were usually spared, due to greater potential for Tying Up Romantic Loose Ends and the fact that they were well-liked characters in general, whereas Rose was divisive even outside of the shipping wars.)
Even more discouraged is throwing Armony and Sophie's names out as Ed pairings. The people who actually have played the games and know what you're talking about will either love/appreciate you, or want you dead. Even though Armony and Ed are pretty canon solely for Broken Angel, it's a small fanbase on the webs.
Possibly the craziest section is the one who ships Ed/Fangirl (or Anyone/Fangirl). Yes, you read that right; wherever you go in the FMA fandom, you're going to find at least a couple crazies who are completely convinced that they are married to Ed or Al, or at least dating them, and that the fictional characters hate the rest of the fanbase for even suggesting other pairings. It's sadly some Serious Business when these folks come out, because at least 70% of the time, they aren't trolling.
The manga fandom itself has had better luck, but wars have arisen between fans who insist that Roy/Riza and/or Al/Mei are Official Couples and fans who insist that there isn't enough evidence to claim that they are. Basically, it's ship vs. no ship here.
Vampire Knight, with Zero/Yuuki vs. Kaname/Yuuki in particular. Is Kaname a creepy and incestuousBastard Boyfriend who wants to dominate Yuuki's life? Is Zero a wangsty moron who gets in between Kaname and Yuuki's True Love? Is Yuuki a "Canon Sue", thus "undeserving" of both guys? This whole ship war between both ships is the reason some fans stopped reading the manga altogether.
The Ouran High School Host Club fandom has conflict between the canon pairing Tamaki/Haruhi and other pairings, particularly Hikaru/Haruhi, but Kyoya/Haruhi is also popular. Some even support the twincest Hikaru/Kaoru pairing.
The Hellsing fandom is usually divided over Alucard/Integra vs. Alucard/Seras vs. Girlycard/Walter vs. Integra/Seras vs...you get the idea.
The whole Alucard/Integra vs. Alucard/(insert other character here) wars is taken to an even further extent when one takes ot3f Kouta Hirano into consideration. Those who support the former pairing point to evidence that there's some sort of hidden romantic attitudes/sexual tension between the two. Those who support the latter pairing point out that the relationship between Alucard and Integra is purely "Master & Servant". And then there are those who believe the relationship is purely ambiguous...yeah...
The issue was that Hirano's statement about the relationship was given five years before the manga concluded as an answer to a person who asked how far will it go, a question that he was nervous to answer (like he would spoil his ending where Alucard returns/isn't dead). He has always been very enthusiastic and supportive about Alucard/Integra (and Pip/Seras) with cover art, complimenting Alucard/Integra Japanese pairing fansites with sketches (before 2chan started vicious wank about him that drove him off the internet), keeping exclusively romantic cosplay pictures of them in his camera during his travels, and making gag fanservice goodies for fans in Comiket. Somebody should ask him now that everything is over. If you dare.
There's also Major/Integra or Maxwell/Integra vs. Alucard/Integra and Pip/Seras vs. other Seras pairings. Not in the Japanese/Chinese/Korean fandoms, however; they seem to be generally chill about pairings and shipping in general.
It's still pretty quiet for now but shipping wars are pretty common in Amagami SS. Even though every single girl gets 4 episodes an arc. It's gotten to the point that the shippers are getting withdrawals due to the fact that they can't bash somebody due to the fact that they're not the love interest of that arc.
The Ship-To-Ship Combat in Ore no Imouto ga Konna ni Kawaii Wake ga Nai! is mostly between the Incest Subtext fans who ship Kyousuke and his sister Kirino and the No Yay fans. Among the No Yay fans, there are fans for Kyousuke-Manami (who consider her the most sane and normal of the choices) against fans for Kyousuke-Kuroneko/Ayase/other girls (who are seen as the more interesting choices).
As a series with a boy with 31 girls as his harem, Mahou Sensei Negima! is bound to have this. Even though Asuna/Negi and Nodoka/Negi are the two favorites, Chisame/Negi got more popular later on, having at least one in-universe endorser and rabid fans who tout it as if it was already canon. However, most of the fights do get ameliorated, mainly because there is one shipping that everyone can agree on: Setsuna-Konoka. God help those who go against this sacred pairing.
YuYu Hakusho: Hiei/Kurama vs. Hiei/ Mukuro. The former wins half the time through ranting and fangirlism, while the latter calmly explains why they should be together (and they generally do a good job in doing so. It helps considering that Yoshihiro Togashi initially was going to have Hiei and Mukuro get together...) Also, Yusuke/Keiko vs. Yusuke/Anyone else. And let's not get started on how many Mary Sues get together with either Hiei or Kurama and begin their own combat...
You don't even need to pit 2/1 and 1/R fans against each other. Go to the "correct" fandom corner and say that Duo should top Heero. Watch the fangirls in that corner tearing each other down about that.
Tiger & Bunny is mostly a peaceful fandom, but it's starting to show early symptoms of this since Kotetsu / Karina and Kotetsu/Barnaby fans have been spotted fighting it out. Is Karina a "girly thus weak" little bitch who gets in between the oh so sacred Ho Yay between Kotetsu and Barnaby? Is Barnaby a selfish, immature Jerk Ass who treats Kotetsu like shit just to satisfy his ego - sooooo unlike the sweet, pretty Karina would? Be careful about expressing such thoughts...
Saint Seiya: in the countries where the anime/manga is popular, there's usually ship wars that go way beyond the levels of verbal hate and acrimoniousness, often expanding itself into Real Life bashing.
The more remarkable examples are the Saint Seiya ship wars of Het Yay fans (fueled by the massive creation of Relationship Sues, once Saint Seiya has too few women on cast) against Ho Yay fans and vice-versa. In several occasions the ship war went to extremes of public detracting of fanwork artists' personal lifes, public menace of aggressions and even real legal offenses.
Not to mention how the fanatical Yaoi fangirls mixed this with What Measure Is a Non-Badass?, trying to erase and deny ANY kind of influence that the few girls in the cast had on the guys, either romantic or friendship-like, just because they thought the girls were all weak and stupid and "not feminist enough to deserve being paired up." Shun/Hyoga shippers were really bad about it, bashing Princess Freya from the filler Ansgard arc despite how much of a Plucky Girl she is and hissing at the mere mentions of Shun's Unlucky Childhood Friend Jun. And the less said about their thoughts on Saori, the better.
To mention: also the pure Ho Yay fandom of Saint Seiya get involved in several bitter ship wars into itself, most noticeably motivated by the debates of "what should be the "right" guys to ship according to what we see" and "what guys are never acceptable to ship together". These can get very, very bloody: i.e. you do NOT go into the path of a Shiryu/Seiya fangirl and tell her Shiryu should go with Mu instead without expecting at least some snark, and at worst nonstop flames.
And last but not least? The purely het side wasn't much better, to be honest. The Shaina/Seiya and Saori/Seiya shippers were horrifyingly cruel to each other and their characters: Shaina was "a stalker and a slutty bitch", Saori was "pathetic, a coward, and not feminist enough". They also liked to bash the crap out of Miho despite how she, in practice, was put firmly in the Unlucky Childhood Friend role.
In the Da Capo anime, Nemu is officially the winner of Junichi with the exception of Da Capo If, in which Kotori wins, mainly because Nemu's dead, since the sequel, Da Capo II, follows their grandkids. However, a lot of fans support some of the other girls since Nemu is usually seen as The Scrappy. Of the other remaining girls, Kotori often gets the most support, since she seems to get along very well with Junichi in the anime.
Durarara!!: Some Shizaya fans will rip out the throats of anyone who mentions Namie or Vorona, while Mikado is just torn to pieces between everyone who wants him as their OTPuke.
After episode 19 of Mawaru-Penguindrum, there has been some seriously fierce ship wars between fans of Kanba/Himari, Shouma/Ringo and Shouma/Himari. It's extremely complicated to explain due to how much of a Mind Screw the series is, but basically it's like this: the third ship didn't have much Ship Tease until the aforementioned episode, and since it goes between the other two, the fans of said "other couples" were seriously thrown off and started warring against it due to possible Ship Sinking. The Kanba/Himari supporters are 'specially loud in their displeasure, due to the Broken Base factor in regards to Kanba the Memetic Badass and Shouma the victim of What Measure Is a Non-Badass?; the other "faction" mainly tends to panic about the possible consequences, but generally don't bash Shouma.
While the Shin Megami Tensei franchise as a whole hasn't been totally devoid of this, Persona 4 has brought pretty big ship wars afloat. As of episodes 9 and 10 (the ones dealing with RiseKujikawa), the shippers have been going rather wild: Rise/Narukami fans (the MC is named Yuu Narukami in the anime continuity) have rubbed the buttloads of Ship Tease they got in the faces of everyone and claiming "RISE END CONFIRMED!" in many forums and Image Boards (specially on 4chan). Which obviously doesn't go well with the Chie/Narukami and the Yukiko/Narukami fans — specially the Yukiko/Narukami shippers, since Yukiko seemed to be the one favored until then. And many panicked in the moment Naoto sorta joined in...
Aquarion EVOL, oh boooooooy. The Zessica/Amata and Mikono/Kagura factions are totaly vicious against the Mikono/Amata pairing. Amata is called "tool" and "ungrateful bastard" for rejecting Zessica's love, Mikono is called "slut" and "weak" for not falling into Amata's arms right away and being confused about Kagura, Zessica is Mary Sue-fied by self-projecting fangirls and fanboys who think Amata owes her cock because she loves him and would sacrifice lots of things for him. On the flip side Kagura is either made into a heartless and evil brute (ignoring how he isn't without his depths), or Marty Stu-fied a la Zessica while his fans insist that Mikono owes him vagina for being his Morality Pet — so her going for Amata instead makes her "a shallow and traitor whore".
Natsu/Lucy vs Natsu/Lisanna. Lucy fans will often point out Natsu's lack of any sort of interest in Lisanna after her return, and fanfics will have her stay dead. Lisanna fans will cite the anime filler scenes that set her up as Natsu's tragic former love interest, their and fanfiction will often have Lucy turn out to have been a shallow replacement for her who is booted from or ignored by the guild upon Lisanna's return.
Erza/Jellal vs Erza/Natsu vs Erza/Gray. Gray and Natsu fans get along pretty well by uniting against Jellal. While he's got canon on his side (he and Erza are the only characters to even kiss thus far, the only main characters to admit to having mutual feeling, the only ones to have a heavily developed romantic history and interactions, the only...) it's easy for Natsu and Gray fans to point out that he's also the only one to have seriously harmed Erza, often claiming that being Brainwashed and Crazy at the time doesn't excuse him because he still physically did it, and it's easy to create a story where Erza comes to that same conclusion and decides to ignore him.
Never EVER ask Madlax fans who is a better love interest for Madlax. If you pick Vanessa, you'll be harshly told that she's dead so she shouldn't really count. If you pick Limelda, people will scream at you that she's an icky Psycho Lesbian who killed Vanessa and doesn't deserve Madlax.
Even worse: bring in a Mutsumi/Keitaro shipper. Say your prayers, everyone.
One Piece, as a No Hugging, No Kissing series, doesn't have that many shippers. However, it is full of deep bonds between characters and sometimes vague interaction between them that could serve as a basis for a potential relationship. Some of the biggest conflicts between the fandom are:
Who Luffy should end up with: Nami, the spunky navigator of his crew, with whom he shares a very deep bond which can be seen as romantic or not with ease — and not to mention Nami seems to be quite focused on other matters rather than whether Luffy will bone her or not. Or Boa Hancock, empress of Amazon Lily Island who fell madly in love with him, although her displays of affection are Played for Laughs and while Luffy is grateful for her help during the Marineford arc, he explicitly stated that "he wasn't going to marry her".
Of course there is also a lot of disagreement on the topic of who Nami herself should be with: the aforementioned airhead of a captain Luffy, girl-crazy cook Sanji or the stoic, serious swordsman Zoro.
Robin also gets some attention from shippers, albeit in her case it is mostly limited to whether she is better fit for Team Dad shipwright Franky or Zoro.
There is also a pretty big following for the coupling of Sanji and Zoro, because of their constant married-couple-like bickering, although these people mostly don't involve in arguments over other pairings for understandable reasons...
Also, there's a small but very loyal corner of Zoro/Luffy shippers who want their own share of deep and mutual trust to go beyond. And not all of them get along with other Luffy-shipping fans.
As of episode 6, it's safe to say that the fragile peace has been broken and we have a full on ship war. After Rin's ungracious reaction to finally defeating Haruka, a good part of the fandom has started SCREAMING for his blood... and unsurprisingly, the leaders of this anti-Rin "movement" are the rabid Haruka/Makoto shippers.
And the "war" has cotinued! Not only that, but a new "shipping faction" might appear since Sousuke Yamazaki, a character from the original novels, is slated to appear in the second season. Naturally, this has brought LOTS of screaming...
Ira/Mako became a popular ship after the Naturals Election. To put it lightly, the disagreements between Ryuko/Mako and Ira/Mako in particular are... not pretty. Especially after the series ended with Ryuko & Mako going on a date, and Mako even kissing her... but then the epilogue shows Satsuki tagging along, and then it cuts to a nervous Gamagoori dressed in a suit holding flowers with Mako approaching. The amount of bile between the two factions exploded, primarily driven by Het is Ew.
Yu-Gi-Oh! ZEXAL. Despite having characters' ages that even younger than the original series, managed to have even more than it. The main Ho Yays of Astral/Yuma, Shark/Yuma, Kaito/Yuma and Rei/Vector/Yuma take the cake.
On the other side of coin there is Yuma/Kotori, Yuma/Cathy, Yuma/Anna and Yuma/Rio.
Tetsuo/Rio and IV/Rio.
Boku wa Tomodachi ga Sukunai gives us the rather ugly war between Kodaka/Sena and Kodaka/Yozora shippers. In other parts of the vast reaches of the internet, there's a battle brewing between those who prefer to see Kodaka with Yozora, and others who would rather see him with Sena; the other girls are largely relegated to Demoted to Extra status in this regard. Amusingly, Kodaka himself keeps letting it slip that Rika is really his type... or would be with a better personality, but that goes for all the girls.