If you suggest that Angel is Buffy's true love and their relationship is tragic and believable compared to the Masochism Tango of Spike and Buffy, the Spuffy shippers will hit you. If you suggest that Spike is Buffy's true love and their relationship was gritty and realistic compared to the hopeless and boring idealism of Buffy/Angel, the Bangel shippers will hit you. This was entertainingly summarised on fandom_wank as: Buffy spent nearly a hundred hours slaying vampires and around 30 minutes shagging two of them. Guess which caused more wank?
If you suggest that Angel and Spike had no interest in Buffy at all except for fighting over her because they're really in love with each other, the het shippers will hit you. If you suggest that neither Spike nor Angel had interest in each other and they both love Buffy more than anything else in the universe, the slashers will hit you.
If you admit to shipping anyone with Riley Finn, everyone will hit you... with the obvious exception of Riley/Xander, which is just common sense — in the comics Xander even admits to being a Team Riley shipper, which makes sense for his character.
Funnily enough, averted with Willow/Tara vs Willow/Oz shippers who generally tend to get along just fine. In their mutual hate of the Willow/Kennedy shippers, that is (yes, all 14 of them). There's also the fact that Oz and Tara are possibly the two characters in the fandom who are the least hated. Granted, both received their fair share of vitriol in the early days (especiallyTara), but nowadays they are almost universally-adored by all fans.
It's probably not wise to bring up Buffy's name when there are Angel/Cordelia shippers about. Nina doesn't fare much better — not since Cordelia was effectively Put on a Bus.
Then there's all the fun that goes on between Wesley/Fred vs. Gunn/Fred vs. Wesley/Gunn vs. Wesley/Lilah shippers. And then when Fred was permanently possessed by Illyria, and you had Fred/Wes fans versus Illyria/Wes fans arguing over which was better. Which is kind of... weird, when you think about it, what with Illyria being a millenia-old demon-god-thingy.
Friends final seasons had Ross/Rachel versus Joey/Rachel with Ross and Rachel fans citing the nine years of history between them, and Joey and Rachel fans arguing their personalities were more compatiable. Most fans just rolled their eyes, tired of Rachel's romantic entaglements. There are still arguments today but they're pretty mild considering Ross/Rachel were end game (as most fans expected) and the Joey/Rachel relationship faded into non-existence. There's also (pretty civil) debate about whether Phoebe should have choson Mike, David or Joey.
One of the oddest ship wars took place between Ross/Rachel and Monica/Chandler. From Season 5 onwards fans argued over not who belonged together (both pairings worked seperately) but which couple was "better". Ross/Rachel fans again armed themselves with history, their super couple status, Will They or Won't They? plotlines, their illegitimate baby, marriage (...and divorce) and endless pining. Monica/Chandler fans pointed out their couple actually made each other happy and stayed together.
The fans of Jake/Heather (Jericho) would argue pretty frequently with the also ship teased Jake/Emily fans. Jake/Emily is canon, Emily is a regular to Heather's guest star, and got far more screentime in Season One. Jake/Heather is more popular, Heather is rather well-liked in the fandom as a whole compared to Emily being at least a moderate case of The Scrappy, and Heather got far more screentime in Season Two. Jake/Emily fans say that they have a history together and have fittingly similar personalities, while Jake and Heather are nothing alike and she's naive and annoyingly perky. Jake/Heather fans say that Jake needs someone who's less trigger-happy, impulsive and angsty than he is, while Jake and Emily have a bad history together, and she's useless, self-entitled and a bit of a Faux Action Girl. Oh, there was even conflict amongst The Powers That Be; John Turteltaub supported Jake/Heather while Carol Barbee supported Jake/Emily. Barbee won.
Rose vs. Martha vs. River bitchfights in Doctor Who fandom get epic, complete with racism, classism, occasionally ageism and sometimes, hilariously, speciesism - some fans are actually capable of arguing that other than the Doctor's true love, all other companions are goldfish to him. Or hamsters. And then some fans follow up on this argument and elevate Doctor/Master to somewhat distressing levels. At large, whenever finding any post at all that discusses the Doctor's love life, the only right response is "in before Fandom Wank".
Of course, there are all of the people who think that the Doctor is asexual, never mind that there was an one shot Love Interest as early as in the episode "The Aztecs" in first season ever back in 1963. There have also been a few arguments between fans of Nine/Rose and Ten/Rose (and yes, even Eleven/Rose). Daleks? Aim for the eyestalk. Sontarans? Back of the neck. Shippers? Run. Just run.
Many fans ship Doctor/Companion no matter what, and god forbid anyone who dares to disrupt this. Mickey Smith, Joan Redfern (to a small degree), River Song, and Rory Williams are often victims of this, along with any companion who is not Rose.
Hannibal: Hannigram vs. Hannibal/Clarice. A one-sided battle as of early season 2, since most of the Hannibal/Will faction has never even heard of the earlier ship much less feels any need to fight with it, while the NMSL crowd is, um, zealous.
Hannigram vs. Hannibloom now, given how the proceedings have turned out. (Will is the one truly akin to Clarice in his courtship with corruption).
Torchwood has this for Jack/Ianto fans who can get quite vicious toward the Gwen/Jack fans. The Owen/Tosh contingent is much saner and calmer.
In the Stargate SG-1 fandom, the two major ship factions were the Sam/Jack faction, and the Daniel/Jack slash faction with Sam/Daniel and Janet/Daniel shippers getting railroaded by both sides.
Stargate Atlantis tended to split between John/Elizabeth and John/Teyla in Season 1. Come Season 2 John/Teyla supporters also faced Ronon/Teyla. (Either Ship Mates of John/Elizabeth or Abandon Shipping John/Teyla fans). Oddly enough, there wasn't much of a war between John/Elizabeth and John/Rodney — the slashers tended to pair her off with Radek Zelenka or Steven Caldwell and portray her as John's BFF Shipper on Deck instead. Come Season 4, it became more like McKeller (McKay/Keller) vs The Internet.
Also, a lot of Eli/Chloe fans jumped ship for Eli/Ginn when it appeared.
While not as severe as many examples, there is tension in the HeroesFandom between Mohinder/Sylar shippers and Mohinder/Matt shippers.
Peter/Claire versus Sylar/Claire versus the fandom.
Sylar/Claire versus Sylar/Elle.
Veronica Mars is the centre of some refreshingly vitriolic flame wars. The two dominant camps are the Logan/Veronica and Duncan/Veronica ones — in spite of Duncan absconding to Australia at the end of season 2 — followed up by the progressively-smaller Piz/Veronica, Wallace/Veronica,Lamb/Veronica, Mac/Veronica and Keith/Veronica. You'd think the latter two didn't exist, but they're out there. Oh yes, they're out there...
iCarly has "Creddie" Carly/Freddie vs. "Seddie" Sam/Freddie. A huge war began in Season 2 when the Sam/Freddie pairing shared their First Kiss, after Freddie had openly pined for Carly prior to that point. The war grew as big Kataang vs. Zutara did, while lasting longer. Both sides declared that Word of God secretly shipped their OTP, that Word of God was pandering to one side before making the other canon, what colour each ship 'owns', timing to the second how long various kisses lasted, thinking too much into freeze-frames and interpretations so involved the Doctor Who fandom would be proud. The height of the conflict extended over a dozen websites and was notable for the entire fandom shifting from LiveJournal over to tumblr and restarting the war there. Carly/Sam also has a significant following that is hated on because they're both girls. It was such an integral part of the fandom that it was turned into an actual war, by the writers, in the episode iStart A Fan War, featuring groups of supporters for the named ships fighting each other In-Universe.
iOMG saw the war continue into 2011 and after the Seddie storyline was indecisive with neither a Ship Sinking or them becoming an Official Couple it has continued into 2012. For a show which started airing in 2007. Not even the finale of the series could stop the war. Sure, Carly goes out of her way to plant a big romantic kiss on Freddie, which he celebrates. But just prior to that event, Freddie had made a joke about 'wanting to get back together' with Sam. Then the creator put in a Flip Flopof God onto his blog about the ending, leaving Creddie fans trying to explain why you wouldn't just romantically kiss someone on the lips to say goodbye, while the Seddie fans cling to the creators explanation about it being a 'goodbye kiss' and hope that Freddie wasn't joking about wanting Sam back.
The war continued onto another show. After the cancellation of Victorious and the end of iCarly, Nickelodeon greenlit a new series, named Sam & Cat. A crossover between Sam, and Cat from Victorious. Which has left the Seddie fandom pushing for a reunion to sink Creddie then give Sam & Freddie a Relationship Upgrade even though Freddie isn't a cast member. Freddie has appeared in two episodes, and attraction was hinted between Sam and Freddie, but they haven't shown any signs of getting back together. It's not inconceivable that with a typical 4 season & Dan Schneider's trolling, the war might have lasted into 2016 or even 2017. A full decade since the original iCarly pilot was filmed.
Not to mention the Carly/Sam shippers vs the Sam/Cat shippers.
However, with the cancellation of Sam & Cat, the Shipping War appears to have ended once and for all.
The House fanbase is a fairly even split between Huddy (House/Cuddy), Hameron (House/Cameron) and Hilson (House/Wilson) all of whom spend a lot of time at each other's throats. All insist their ship is canon, based on purely circumstantial evidance.
It doesn't help that Hugh Laurie himself thinks the show will go through Huddy, Hameron, and Hilson if the show lasts long enough. Or that Robert Sean Leonard (who plays Wilson) has called the House/Cuddy storyline "boring" a number of times.
When Cuddy started dating Lucas the Huddy fans and the Luddy fans got into some serious fights.
And now that Cuddy and House have finally hooked up, shipping wars are usually between Huddy fans ("YES! This is SO overdue!), Hilson fans ("Ugh, not Cuddy! She sucks! HOUSE/WILSON FOREVER, BITCHES!") and the non-shippers ("I knew this show was going downhill! That's it, season 8 is NOT happening!"), with everyone accusing the other of being losers ("Huddies are brainless fangirls!" "Hilsons are delusional yaoi fanfic writers!" "Non-shippers are romanceless and blind!") And yes, you can expect every group to claim to be the majority.
House and Thirteen seem too have waaaaay too much chemistry for it to be just a coincidence. Then again, even Chase and Thirteen do. Maybe she is just that way with everyone.
It appears that House/Wilson may have emerged as the unlikely victor in this shipping war after all, since House faked his own death and literally rode off with Wilson into the sunset at the end of the series finale.
Chase and Foreman receive lots of hate from Cameron/Thirteen shippers for their respective involvement in Chameron and Foreteen. Surprisingly, it goes both ways, with Cameron and Thirteen receiving hate from Chase/Foreman shippers, for their involvement in Chameron and Foreteen.
LOST: Jate and Skate shippers continue to be locked in battle.
And in Season Five, the writters decided to add Suliet into the mix.
Everyone always forgets poor Jacket!
Not to mention the Desmond/Claire vs. Charlie/Claire shipwars that happened in the earlier seasons, and the Michael/Sun vs. Jin/Sun shipwars...in fact, why don't you just go look at the season 1 Lost promo for the UK on YouTube; it's a minute and a half of beautiful ship war dancing.
Firefly shippers of River/Mal and River/Jayne are locked solidly at each others' throats, if only because both of them have about the exact same amount of canon support for their respective ships, and it's probably a good idea to keep both sides isolated from the River/Simon shippers.
For that matter, the Simon/Kaylee and Jayne/Kaylee shippers don't really see eye-to-eye on a lot of things. Can't imagine why.
Suggesting that Nandi might have been better for Mal than Inara tends to really annoy the Mal/Inara shippers.
And once you add Ship Mates into the mix, the whole thing escalates into a full scale war between the Mal/Inara-Simon/Kaylee-Jayne/River alliance and the Mal/River-Jayne/Kaylee-Simon/Inara faction. And that's without even getting into the rivalries between popular slash pairings like Mal/Simon and Jayne/Simon or River/Kaylee and Inara/Kaylee.
And god forbid shipping the crazy underaged broken girl with anyone Squick you out.
If you ship Simon/Inara, Jayne/Kaylee and Mal/Zoe, the Jayne and Wash fangirls will hunt you down.
Strangely enough, if you ship Wash/Zoe you're safe from all sides. Probably because they're the only canon ship, and Joss gave them very lovely scenes together which left a lot of viewers pleased with that ship.
One Tree Hill fandom has an ongoing Brooke/Lucas versus Peyton/Lucas ship war, despite the fact that Brooke/Lucas ended their official relationship in S4 and Lucas/Peyton ended the show together.
Gossip Girl fandom has become somewhat of a Broken Base between fans of Chuck and Blair versus Dan and Blair. Chuck and Blair had been declared endgame by Word of God but when Dan and Blair was introduced in S4 (romance in S5), many fans immediately loved the pairing.
This ship war largely centers over perception of Chuck and whether he is a Jerkass or a Woobie after he (among other things) traded Blair for a hotel (yes this was a plot) and had a few Crazy Jealous Guy moments but also a possible redemption arc, depending who you ask.
Less vocal are other smaller shipwars like Nate & Serena versus Dan & Serena (both couples are Highschool Sweethearts ). The Blair pairings however seem to be the most popular in the fandom.
Don't forget the Nate and Serena vs. Nate and Jenny.
As of the finale, Blair and Chuck and Dan and Serena each got married with Nate and Jenny single (leading writers to Pair the Spares)
Back in the early ages of fandoms and fighting, there was the JAG Shipping wars. All pairings were argued but beware and prepare if you favoured anyone currently going out with either Harmon Rabb or Sarah Macenzie.
Smallville. The Clanaphiles, the Cloisers, and the Chlarkers have all been at each others' throats. More recently, since Clois and Chlollie gradually became the more dominant ships in and out of universe, many of the remaining Chlarkers have been at the Chlolliers' throats as well. The Clexers, on the other hand, are split between enjoying their Ho Yay while engaging in Pass the Popcorn on the other shippers' Flame War, and rabidly dedicated to the mission to depict all females and non-supervillains within ten miles of Clark Kent as vicious shrieking Yanderes or total morons. The Cloisers have also largely engaged in Pass the Popcorn with one another while the non-canonical ships duke it out.
The various shipper groups in the Smallville fandom have also been known to fight in proxy wars on behalf of ships that serve as Ship Mates to their own One True Pairing. For instance, Clois shippers were often allies with the Chimmy shippers from Seasons 6 through 8 because it kept Chloe away from Clark, so it felt right to support Chimmy (the Chimmy shippers didn't always reciprocate the good will though. Some Chloe supporters shipped Chimmy merely because they felt that Clark—the future Superman—didn't "deserve" the supposedly-saintly Chloe). Similarly, some Chlark shippers supported Lollie because it got Lois away from Clark.
The Ship-to-Ship Combat in the Smallville fandom even extended to arguments over the amount of screentime each potential love interest received. If Lois was getting a lot of screentime, the Chloe/Clark shippers would scream that the writers were somehow destroying Chloe to make way for Lois. If Chloe was getting a lot of screentime, the Lois/Clark shippers would complain that Chloe was a "waste of time" because she wasn't in the Superman comics (she is now though). And if Lana was getting a lot of screentime, EVERYONE outside of Lana's small-but-devoted fandom would complain. Ironically, a lot of these shippers didn't seem to even care that much about Clark; they simply viewed him as some kind of trophy to be awarded to the "best" girl.
The Big Bang Theory fans argue whether Penny should be dating Leonard or Sheldon. A third faction insists that both pairings detract from the quality of the show. However, since the (majority of) the fans try to maintain a level of civility, it's more of a Cold War than an all-out firefight.
In Supernatural fandom, the Sam/Dean and Dean/Castiel shippers have been butting heads since Cas first showed up at the beginning of Season 4 and introduced possibly the first significant competition for Sam/Dean's popularly-held Fan-Preferred Couple status.
And then there's the rise of Sassy (Sam/Castiel) as a non-crack ship circa Season 6.
Which has only gotten stronger in Season 7, becoming even less of a crack pairing. However, most Sassy shippers have the sense to stay on the fringes of the fandom and avoid the firefight between Wincest and Destiel.
In The Vampire Diaries fandom, there is an intense rivalry between Stefan/Elena (Stelena) shippers and Damon/Elena (Delena) shippers. Between the two fan groups, it appears as though Stefan/Elena shippers are much more quiet, calm and less vocal (but still a large, solid fan base), while Damon/Elena shippers are much more loud, vocal and even "rabid" about their ship, believing that their loudness and vocality might have an influence on Damon/Elena possibly becoming a couple on the show. Sometimes the shipper wars between Stelena and Delena often turn into Salvatore brother wars, with Stefan fans sparring with Damon fans.
Another shipper war taking place in the TVD fandom are Tyler/Caroline (Forwood) shippers and Klaus/Caroline (Klaroline) shippers.
Another huge shipper war occurred in season five between Stefan/Elena (Stelena) fans vs. Stefan/Caroline (Steroline) fans vs. Stefan/Katherine (Steferine) fans. Season five was basically a mega war within the fandom about who Stefan should be with. Poor Stefan. That is what he gets for being a Launcher of a Thousand Ships and seemingly being the "fan favourite" of the audience throughout the season.
As of season six, the season has only begun and there is already a very intense and heated rivalry between Stefan/Caroline fans and Stefan/Elena fans. There has been a hint that there might be a Stefan/Elena/Caroline love triangle this season, which only heats up the intensity of the rivalry in the fandom. Although, there are still those pesky and disgruntled Stefan/Katherine fans who don't want Stefan to be with either Elena or Caroline.
Another shipper war going on in season six is the one between Stefan/Caroline fans and Enzo/Caroline fans.
There's also a shipper war brewing between Damon/Elena fans and Damon/Bonnie fans.
The Secret Life of the American Teenager has Ben/Amy vs. Amy/Ricky vs. Ricky/Adrian and even Adrian/Ricky vs. Ricky/Grace vs. Grace/Jack before Ricky and Grace broke up in Season 2 and Grace got back together with Jack.
And yes, the writers play with all of these shippings and more. In fact, it's essentially the premise of the entire series. However, the biggest factions seem to be Amy/Ricky vs. Amy/Anyone else and Ricky/Anyone else.
The re-imagined Battlestar Galactica had some serious Anders/Starbuck vs. Lee/Starbuck wars. Apparently there were a lot of fanfics that depicted Anders being unfaithful to Starbuck whereas in the show, it was the other way. Thankfully most people abandoned it after the obnoxious love square of Season 3 in favor of the more solid and certainly more pleasant Roslin/Adama relationship.
Skins fans have a bizarre war going on between two completely canon and perfectly compatible ships; Freddie/Effy and Naomi/Emily. The war turns out to be rooted in the amount of screen time and importance the show gives to each (Naomily were the Beta Couple in S3, but Freffy became more Beta-like in S4). Freddie being murdered by Effy's psychiatrist with a baseball bat in Effy's S4 episode has resulted in somewhat of a cease fire, though, as the two camps united against the common enemy.
Effy/Freddie vs. Effy/Cook counts as well.
Similarly, Glee has a war between Finchel and Klaine despite the fact that both work together. It's not a fair fight considering thst B outnumbers A at least 3 to 1 and isn't even Rachel's biggest fanbase
Try to have any discussion about any character in Robin Hood and you'll probably end up in a Shipping War about whether Marian should have married Guy or Robin. Guy fans argue that Guy/Marian had more chemistry, highlight Robin's faults (arrogance, impatience, immaturity) and downplay Guy'sindiscretions (burning Marian's house down, threatening her with execution, dumping his infant son in the woods, killing innocent peasants, among many more). Robin fans cite hundreds of years worth of legend, the fact that Marian chose Robin of her own free will, that Guy stabbed her to death with a giant sword, that Robin and Marian get a Together in Death scene, and that Guy himself eventually admits to Robin that "she was always yours." And the debate still rages...
The Merlin fandom tends to be divided in slash and het camps— those who think Merlin and Arthur are fated to be, and those who don't. The het camp was mainly comprised (in the beginning) by Arthur/Morgana, Merlin/Morgana, and a smaller faction of Lancelot/Gwen shippers, and all these factions were relatively civil to each other. However, the writers did not help matters any by giving the characters' relationships a drastic turn-around in series two and declaring most of these ships Doomed by Canon via the inclusion of the (mostly non-existent in series 1) Arthur/Gwen ship, complete with True Love's Kiss and everything. This resulted in most of the other shipping camps putting down not only this ship but the show as a whole for reasons varying from "bad writing," to "feels forced," to TPTB not being bold enough to deviate from the original Arthurian myth. Arthur/Gwen shippers, not to be deterred, arm themselves with canon to defend their ship, making the ship debates hark back to times Older Than Print. Nowadays a lot of the fans involved have left the fandom in disillusionment at the reasons above-mentioned, so it hasn't been quite as bloody as it could've been, but the potential remains as those still loyal wait for the start of series 3 in 2010.
With the conclusion of series 3, the shipping war finds itself in a bizarre stalemate. Arthur/Morgana was well and truly sunk with the revelation that the two of them are half-siblings, and Merlin/Morgana took a bit of a battering due to the fact that Morgana is now trying to kill everyone (though the two make up for it thanks to the insane amounts of Foe Yay between them - this scene is widely known as "the eye-fucking in the woods"). After what was initally a case of Strangled by the Red String, the writing of Arthur/Gwen significantly improved, leading to a wider acceptance of these two as a couple (as well as a Flash Forward to Guinevere's coronation that more or less cemented them as end game). However, the reappearance of Lancelot at the end of the season has led to many Arthur/Merlin shippers hoping that the legendary Love Triangle will take place so that Arthur turns to Merlin for comfort. However, since this is Saturday night family programming, the odds of that happening are practically nil.
End of season four update: Sure enough, the Lancelot/Guinevere liason was the result of an enchantment and Arthur and Guinevere got married at the end of the season. Latest reports from the set of season five have indicated that Guinevere will have a more prominent role in the show now that she's Queen of Camelot, and that she'll be Arthur's main confidant. Merthur fans have not taken this particularly well, and some are complaining that her presence is going to ruin the bromance dynamic.
Things got a bit hairy within the fandom of The Sarah Connor Chronicles once the John / Cameron ship's popularity became more prevailant. Some fans found the idea of John Connor, the man who smashed Skynet being a Robosexual to be inherently squicky. Detractors would latch on to whatever alternatives they could find, as long as they weren't metal. First it was John/Cheri, then it was John/Riley, finally John/Allison before the series was abruptly canceled. You even had some who clung to the idea that Kate Brewster would eventually show up and re-establish Terminator 3'sOfficial Couple, despite the fact that in TSCC's contnuity John would be a bit young for her (due to Time Travel).
Not quite Ship to Ship, but Star Trek: The Original Series fandom has been arguing for decades about whether Kirk and Spock are lovers or just very close friends. Shippers accuse non shippers of ignoring the "glaring" subtext, non shippers accuse the shippers of "ruining" a great platonic friendship. You'd think people on both sides would've agreed to live and let live by now.
On the other hand, Kirk/Spock versus Spock/McCoy tends to be a pretty laid-back argument (which, it must be said, frequently culminates in the agreeable solution of having a threesome).
And when Buzzfeed weighed in with their support for Rory/Logan, the comments predictably started fighting over which of the three boyfriends were the best for Rory.
The problem with Law & Order in any of its incarnations is that no-one ever gets together, ever, so the fans have to run with the subtext. And how. Arguably the best example is the approximate 50/50 split in the SVU fandom between Alex/Olivia and Elliot/Olivia, which, fuelled by the fact that both ships have had a lot of Ship Tease over the years, can get fairly heated.
But while the producers have sunk the Elliot/Olivia ship repeatedly, Stephanie March has made the Alex/Olivia fans very happy. In an interview with After Ellen, not only is she not freaked the hell out by the Les Yay implications, but admitted that she thinks it's possibile that Alex and Olivia are in love, and that they may have been having a Grissom/Sara-eque quiet, offscreen relationship. We now have yet another reason to love you, Stephanie March.
An odd example has occurred in SVU fandom now that a couple actually has gotten together: Detectives Amaro and Rollins have been established as having an affair. Some shippers of Elliot and Olivia are pissed off, not because it's a threat to their ship (because it isn't), but simply because it's not fair that Amaro and Rollins get a hookup when E/O never did. What's funny is that a lot of fans whose ships have actually been sunk by this hookup (Benson/Amaro and Fin/Rollins) have so far been a lot more calm about it.
Xena had some incredibly intense shipping wars between Xena/Gabrielle and Xena/Ares due to its spillover into real-world issues of LGBT rights and representation. In a time when there was virtually no positive LGBT representation on television, the implied relationship between Xena and Gabrielle was all that viewers had. Picking up on this, the writers and actors played up the subtext. Xena/Ares and other shippers denounced this as Pandering to the Base. Xena/Gabrielle shippers, or "Subbers" often interpreted this as homophobia.
Degrassi's Season 9 movie seemed to spark this, as the canon pairing became Spinner/Emma which annoyed all Sean/Emma and Spinner/Jane fans. Before that, there was Sean/Emma vs. Sean/Ellie, Sean/Ellie vs. Craig/Ellie, Craig/'female character' vs. Craig/'female character' vs. Craig/'Male character', Declan/Holly J vs. Spinner/Holly J, Declan/Holly J vs. Declan/Clare, Eli/Clare vs. K.C./Clare vs. Declan/Clare vs. Jenna/Clare... I could go onm but I would break the page.
Forever Knight has had 14 Ship Wars as of November 2011, and each take place as a virtual convention in Fan Fiction format on the fandom's main list, http://forkni-l.psu.edu. There are several "factions", grouped by favorite character or ships of said characters, and each factions name refers to those groups. "Knighties", for example, are fans of Nick Knight, the main character, "Cousins" are fans of "Uncle" Lucien La Croix, the Nick&Nat Pack are those that ship Nick and Natalie, and so on. The authors write for themselves and each faction writes for its character of focus. Each of these wars are meant to be fun, there is very little serious Die for Our Ship.
The first signs of Ship-To-Ship Combat for Super Sentai appear to have begun with Hikari Sentai Maskman, where more than twenty years on debates are still raging over whether Red Mask (also named Takeru!) should end up with Iyal, Momoko or Haruka.
Tokusou Sentai Dekaranger has an ongoing debate over Hoji/Jasmine vs Tetsu/Jasmine; the former group of shippers trying to push Hoji and Jasmine's positions as the most "pro" and "senior" of the team, the latter group arguing that Hoji is still hung up on his ex, Teresa.
In the source material, the Ship-to-Ship Combat between the Chiaki/Kotoha shippers and the Takeru/Kotoha shippers was understandable because there was what could reasonably be interpreted as Ship Tease for both pairings in the series. However, Emily has shown no discernable romantic interest in Jayden, nor he in her, so the fact that there are even Jayden/Emily shippers is puzzling to begin with.
Some Jayden/Emily shippers admit to being general Red/Yellow shippers (whether or not the Sub Text even exists) out of their general dislike of the frequent Red/Pink ship (whether or not the Sub Text even exists). Some of these shippers also cop to being Takeru/Kotoha shippers who hoped that a Jayden/Emily ship would have been a sort of second chance for Word of God to give their chosen ship validation. Given that Word of God has all but declared Mike/Emily official, it would seem that the Chiaki/Kotoha shippers were the ones who got the second chance.
For Mighty Morphin' Power Rangers, there is the ever-infamous war between those shipping Tommy/Kimberly and those shipping Tommy/Katherine, mostly driven by fans of the former who hated having their ship sunk. This has, in turn, caused angry retaliation from the latter faction. Then oddly enough, you occasionally get Jason/Kimberly shippers that consider Tommy to have been a Marty Stu that "stole" Kimberly from Jason. Tommy's reappearance for Power Rangers Dino Thunder introduced Tommy/Kira shippers as a third faction in the combat.
In Kamen Rider Fourze, Ryusei's most constant love interest is Tomoko (who is ostensibly his girlfriend by the time of Movie Wars Ultimatum, set five years after the events of the show) but two other women (Inga Blink and Shirakawa) had romantic interest in him, leading to arguments over which one he should have ended up with.
Kamen Rider Gaim: Kouta/Mai and Kaito/Minato vs Kaito/Mai. Anyone/Mai vs the various slash ships.
In the NCIS fandom, Gibbs/Tony slashers and Tony/Ziva shippers hate each other. Violently. G/T fans also like to make Ziva Die For Their Ship. Kate doesn't get nearly as much flak.
Glee. Good Lord, where to begin? Thanks to the Love Dodecahedron nature of the show, any given character will have a fair number of onscreen relationships (both actual romances and subtext). ALL of which have their diehard supporters who will raise hell if their favorite pairing is broken up (or never started at all in the case of subtext). A particularly nasty ship war that comes to mind was in the second season between Brittany/Santana and Brittany/Artie, complete with accusations of But Not Too Gay for making Brittany date a boy, But Not Too Bi for making her stay with Santana in the end, and Unfortunate Implications for how Santana convinced Brittany to cheat on Artie with her, and whether or not Artie was justified in lashing out at Brittany which caused her to break up with him. This is but one example of the bitchfights between shippers. The forum battles get epic.
Tinsel: Team Kwame vs. Team Soji over Telema Duke. The fandom can get quite vicious at times with Team Soji fans labelling Team Kwame fans liars and Team Kwame fans calling their rivals wimps.
Usually averted in Criminal Minds fandom, largely due to the fact that since Haley Hotchner was killed there are precisely no canon ships to get invested in. The conflict is, instead, between those who want ships in canon and those who don't. However, a scene or two that appeared to hint about something shippy possibly developing between Reid and Ashley Seaver at some point in the future galvanised a certain Anti-Ship Combat from those who specifically didn't want that ship happening.
Soap Operas in general are the source of some of the most heated shipping wars in existence, and the extremes that some shippers go to can get pretty damned creepy.
The X-Files: The early years of the show's run coincided with the Ur days of wider-spread internet use, and whole message boards and mailing lists could be devoted to ship wars. Pick any conceivable pairing and somebody shipped it, so the battles could get entertaining and really, really confusing. Disparate ships would sometimes unite against a pairing they considered a common foe, and even message boards supporting the same ship could wind up at war over some minor disagreement. Shipping could be some Serious Business in the fandom. Then there were the noromos (short for 'no romance') who objected to shipping in general, especially as the series went on and it became more blatant between Mulder and Scully. Their chief complaint was that they felt it got to the point where it detracted from the plot. They went to war with absolutely everybody.
A fanwar was attempted on Fanfiction.net for Suite Life On Deck between Cody/Bailey (Cailey) and Zailey (Zack/Bailey). It managed to be avoided when initiator was revealed to be a Cailey shipper posing as a Zailey shipper.
This broke out in CSI NY fandom, though it was more of a case of "many ships against one ship" in the case of the Danny/Lindsay ship (Danny/Flack, Danny/Angell, Danny/Rikki, and Danny/anyone-but-Lindsay vs. Danny/Lindsay). Claims of no chemistry, lack of believability, excessive screentime, were among the arguments flung against Danny/Lindsay by the anti-D/L faction, compounded by their general dislike for Lindsay as a character.
Mac is also in the middle of this, with Mac/Jo vs. Mac/Stella vs. Mac/Christine vs. Mac remaining single, eternally mourning Claire. Mac/Peyton is the exception because Peyton is generally regarded as The Scrappy. There is a Mac/Lindsay faction, plus the inevitable slash ships, but the four previously mentioned groups are the primary combatants.
CSI: Crime Scene Investigation had conflict over Grissom/Sara, mainly from Grissom/Catherine, Sara/Nick and Sara/Greg at the beginning, but Grissom/Catherine sort of tapered off afterwards, following this, it never narrowed down into one ship against another, it was more another 'many ships against one' thing.
Bones Do not try to argue in favor of Brennan/Sully to a Booth/Brennan shipper.
The A-Team has had near-constant conflict between two primary ships - Hannibal/Face and Murdock/Face. While all out ship wars arenít the norm for this fandom, fans are still extremely defensive about their OTPs, with a simmering Cold War of sorts stretching back to the mid-80s. The argument, however, usually seems to be mostly concerned with who Face happens to be sleeping with on the team. Both camps tend to cite a plethora of examples from episodes as to which ship is better supported by canon, despite the fact that the show contains roughly equal amounts of unintentional innuendo from Hannibal, and inappropriate touching by Murdock. Murdock/Face, however, typically wins out as most popular.
This problem has been further compounded by the 2010 movie, which most new fans claim more heavily supports Hannibal/Face, or even B.A./Face or Sosa/Face (gasp!), over Murdock/Face, leading to tensions with the old fans of the show.
Some fans choose to bypass this conversation altogether, and go for a Hannibal/B.A./Murdock/Face ship instead, although this, again, is more common in the movie fandom.
Even a relatively obscure fandom like The Addams Family isn't safe. A ship war that began with the advent of the Broadway musical pits Wednesday's adolescent crush Joel (from the second movie) against her fiance Lucas (from the musical). The factions might as well be re-named "Those Who Haven't Seen The Musical" and "Those Who Have" respectively.
In the Hollyoaks fandom, there is the Stendan VS Stug war which raged on to disturbing levels, where even side ships that didn't take place (Bruglas shippers) got attacked. Now that Stendan won, but Brendan has gone off to prison for the foreseeable and Stug has been pronounced dead (regardless of being married still), the Stendan shippers have turned their hate to anything Doug related, which is his new pairing with John Paul, which sees the end of Mc Dean and who knows when this will end.
Pretty Little Liars has two. Aria/Ezra vs Aria/Jason and Emily/Paige vs Emily/Alison (there used to be a third faction of Emily/Maya, but that died off when Maya did). The latter can get really heated.
In the Gilligan's Island fandom, as mentioned in the main page's quote, there's severe rivalry over who Mary Ann belongs with—Gilligan or the Professor. With Ginger, there isn't as much—Mary Ann/Gilligan shippers often favor Professor/Ginger, while Mary Ann/Professor ones may opt for Ginger/Skipper or Ginger/Gilligan.
The Once Upon a Time fandom rocks this trope with the love life of poor Emma Swan. Though Emma herself is most concerned with her son, the fandom battles bloodily over whether she'll end up with Hook, Neal, or ReginaMills, particularly for the first two. Shippers will go as far as to try and boycott an episode heavily featuring a rival ship or harassing the writer's twitter if the show doesn't go in the direction they'd like, which has gotten even worse now that the Hook/Emma romance has gotten more media attention than the Neal/Emma romance ever did. Its gotten to the point that practically every third post on any given ship's tag on Tumblr is just telling everyone to calm the fuck down.
In addition to this, there is the interesting case of Rumple/Belle shippers not getting along with Emma/Hook shippers
Similar conflicts currently plague The Walking Dead mainly between shippers of Daryl/Carol and Daryl/Beth (neither of which has gotten beyond Ship Tease canon-wise) with a small handful of Daryl/Michonne and Daryl/Rick into the mix.
If you are a fan of House of Anubis who believed that, in the second season, Joy and Fabian were a better pairing than Nina and Fabian were, you would not last long before getting flamed. This ship-war started at the end of the first season, when Joy wasn't even a main character and had not even done anything yet, which Nina/Fabian shippers would often ignore and paint her as a bad guy anyways. The Nina/Fabian shippers had Canon on their side, and argued that Nina and Fabian had always liked each other, that the pairing was too popular to be sunk (season 3 events non withstanding) and pointed that everything Joy was doing ruined her chances. On the other side, Joy/Fabian shippers claimed that Nina was abusive and Joy would have been nicer to Fabian in the long run, that Joy and Fabian were best friends before the events of Season One, and that they had better chemistry. Things seemed to have calmed down in the third season, however, just to make way for a new (but less vicious) war between the Patricia/Eddie shippers and the KT/Eddie shippers, which lost some steam on the KT/Eddie side when it became obvious that Eddie still liked Patricia and KT was not going to try and do anything that would hurt Patricia.
Arrow generally has a fairly mellow group rshippers, with Oliver/Felicity and Oliver/ Sara shippers generally cool with each other and united in their dislike of the Oliver/Laurel pairing. That being said, smaller segments of all groups (with the pro-Felicity and anti-Laurel contingent in the lead) can get rather nasty at times.
Although Agents of S.H.I.E.L.D. has several love triangles, it seems like the one causing the biggest divide centers on Jemma Simmons: you have those who prefer her with Triplett versus those who want her to respond positively if Fitz ever manages to admit his feelings to her.
Come the second season, battle lines are being drawn between Fitz/Simmons and Fitz/Mack.
This sprang up in How I Met Your Mother with the finale. If you were a fan who believed that, in the series finale, that Ted deserved to get back together with Robin after the death of the mother, you would not last long before getting flamed by both Ted/ Tracy(AKA the Mother) and Robin/Barney shippers, both of which were sunk in the finale. The latter argue that their pairings had better chemistry, had more canon support, and were genuinely much more developed, and that the show itself railed against a relationship between Ted and Robin for 9 STRAIGHT YEARS, and as such undos the Character Development and key themes for the entire series, and ended up inferring that Ted never loved Tracy at allnote this has actually gotten to the point where diehard Robin/Barney shippers have accused one of the creators of the show of misogyny and inability to move on from his own childhood men's fantasies, through there isn't any evidence to either of this. The former argues that Ted needed to move on after mourning Tracy's death for 6 years, that the final scene never inferred he didnít love Tracy, and that that the Ted/Tracy and Robin/Barney shippers wanted a naive and happy sugar-coated unambiguous Disney Ending that goes against the Show's Themes. Giving the reaction to the finale, take a guess which side is the most predominant in the fandomnote and the predominant side actually ended up winning in the long run considering the nature of the official alternate ending.