In Akame ga Kill!, Tatsumi ends up with Mine, the Night Raid sniper. While some fans were happy about them being together, some still preferred the concept of Tatsumi being with someone else:
The titular assassin Akame is the main pick for the fan-preferred pairing with Tatsumi. Unfortunately, this may be Incompatible Orientation as Akame was known to show feelings for an assassination target she had once: Merraid Oarburgh. So she may be a lesbian.
A third great pick is Chelsea, due to being (usually) much nicer than most of the cast, as well her canon crush on Tatsumi. This ship was sunk as well due to the Anyone Can Die nature of the story, as Chelsea suffered the most undeserving and horrifying death in the whole series shortly after being introduced.
A lot of Aquarion Evol fans, at least in the U.S., preferred Amata to be with Zessica and Mikono to be with Kagura.
From Ashita no Nadja, at least half of the fanbase will tell you that Kennosuke is that much of a more fitting match for Nadja. It helps that Nadja's Love Triangle-y canon interest on Francis/Keith (Black Rose) is mostly based on a "he saved me, therefore I love him" reaction, while her friendship with Kennosuke was actually developed and detailed.
In the Binbogami Ga fandom, the Pixiv fanartists are very much in favor of Ichiko and Momiji over the former's canonical love interest Keita.
Most Black Butler fans ship Sebastian/Ciel, even Word of God repeatedly state that they are only using each other for personal gain. As for their canon romantic options, Ciel is engaged to Elizabeth, while the only thing Sebastian genuinely loves is cats.
As the two primary main cast characters, Ichigo/Rukia is extremely popular among fans even though Word of God has stated that their relationship is "close, but not romantic". The anime also supports this ship and inserts a lot of filler material to give them Ship Tease that doesn't exist in the canon material. The Distant Finale revealed that Ichigo and Rukia respectively married Orihime and Renji, much to many a fan's consternation.
The major slash pairings are Ikkaku/Yumichika, Kyouraku/Ukitake and Yoruichi/Soifon. Canonically, the first two are both Heterosexual Life-Partner examples and the third is a mentor/student Undying Loyalty relationship. However, both the fandom and the animators love shipping them together and find any excuse to do so.
Daikichi and Yukari from Bunny Drop are this. They have their Ship Tease and fans find the idea of two single parents up together adorable, however come the manga timeskipand it turns out it didn't work between them due to the fact Rin and Kouki end up dating. The manga's Official Couple is Daikichi and Rin, the kid he's been raising since she was six. Both the anime adaptation and Live-Action Adaptationignore the manga and leave open endings with plenty of implications that Daikichi and Yukari will end up together.
Cage of Eden: Akira/Mami has started rapidly gaining popularity, even though Akira/Rion was the official pairing.
Cardcaptor Sakura has Eriol/Tomoyo, even though Eriol/Kaho is canon, and Tomoyo is in love with Sakura. But many fans will pair them because of their similar personality traits and that they find Eriol dating Kaho to be "creepy" because of their apparent age-difference (Word of God has stated though that Eriol is Fujitaka's age, technically making him older than Kaho and way older than Tomoyo).
And when it comes to slash ships, Lelouch/Suzaku is the most famous and has the most fan material. It helps that the creators and marketing team caught on to this and released quite a lot of homoerotic official products of them.
Cowboy Bebop: Spike has a canon love interest in Julia, but the majority of fans prefer him with Faye. It helps that Word of God has confirmed Spike and Faye had a thing for each other, but Spike's obsession with his past prevented him from doing anything about it.
Fans of Da Capo are rather divided about who Jun'ichi should have ended up with, but most think Kotori would have been a much better match for him than Nemu for various reasons, among them not being a Tsundere or his adopted sister. Unfortunately, the sequel reinforced the official pairing by featuring Jun'ichi and Nemu's granddaughters. (An alternate-universe OVA was released in which Kotori wins. Kotori must have been pretty popular.) In the original VN, Nemu has almost an unrecognizable personality if you're only used to her in the anime (she's far less bitchy and far more empathic and likable). She was undoubtedly the favorite of the majority until the anime adaptations.
Danganronpa 3: The End of Hope's Peak High School had a ship war between the 74th Class trio. Munakata/Juzo vs Munakata/Chisa vs Juzo/Chisa, being that there were heavy implications that Munakata and Chisa were an Official Couple. Ultimately, with The Reveal that Chisa was a Remnant of Despair who had been actively pushing Munakata into despair and took part in killing Chiaki and Episode 10 of Side:Despair revealing that Juzo was in love with Munakata, ultimately, doing a Heroic Sacrifice and saving the last participants of the Final Killing Game in exchange of bleeding to death, Juzo/Munakata quickly toppled the other two ships.
In Date A Live, while Tohka is the lead girl, fans would prefer shipping Shido with Kurumi since they snark so well with each other.
Detective Conan: During the early parts of the series, it was heavily implied that Shiho/Ai, was in love with the main character Shinichi/Conan. Both characters had personalities that fans found complemented each other more naturally with the whole Deadpan Snarker schtick. However as the series went on, the creators almost completely erased all mention of Shiho/Shinichi Ship Tease material and now, theyre just True Companions. A large majority of fans of the series still prefers Shiho/Shinichi due to how their personality plays off each other as opposed to the canon Ran/Shinichi.
Digimon: With its dozens and dozens of characters over the years, there's been all sorts of contention. Digimon fans grew up with the rise of the internet, so these are some of the earliest Fan Preferred Couples online.
In a rather infamous example of Relationship Writing Fumble and Depending on the Writer, Taichi and Sora became a vastly more popular couple than the canonically-intended couple of Yamato and Sora. Show director Hiroyuki Kakudou had always planned for Sora and Yamato to end up together, with Sora and Taichi simply being Just Friends. Sora and Yamato being married with kids was even a part of the original finale to Adventure but he scrapped this as he thought the characters were too young. Even the production staff appeared to ship Sora with Taichi instead as they admitted they were used to the main boy ending up with main girl (which was a cliche that Kakudou himself was specifically trying to avoid) and some of the voice actors expressed a preference for Taichi/Sora (including Mayumi Yamaguchi, the VA for Yamato's Digimon partner Gabumon). Mamoru Hosoda, who directed Our War Game seemed to imply that Sora had a crush on Taichi, although this "crush" was never a thing in the original Adventure and 02. Naturally, the fans were all thrown for a loop when Kakudou forced the issue by having Sora and Yamato become a couple during the 02Christmas Episode despite their relative lack of relationship development prior. This is much worse in the English dub, which put in a lot of Ship Tease for Tai and Sora which was never there in the Japanese versions and Jeff Nimoy (the man in charge of the dub) has even apologized for changing up the script so much. The lack of romance in Adventure meant it was possible for Sora to have ended up with anyone and the Yamato/Sora relationship went over with Japanese audiences much easier than it did with Western ones as a result (it also enjoys a much warmer reception in other countries with dubs more faithful to the original Japanese version, such as in South Korea). Later sequels and video games such as tri. and the PSP video game attempted to spin the Yamato-Sora-Taichi relationship off as a Love Triangle because of how inconsistent the writing has become.
Takeru and Hikari (Yamato and Taichi's younger siblings, respectively) were the show's most popular Toy Ship, period, which unfortunately led to some vicious Ship-to-Ship Combat when 02 fashioned a Love Triangle with them and newcomer Daisuke, though Takeru remains the more popular suitor, if only because he's the incumbent.
While Ken and Miyako wound up married in the finale, most fans shipped Ken with Daisuke instead, since they have very little in-show support other than her having a massive crush on him that he generally didn't notice much, as well as the Foe Yay between Ken and Daisuke, while Ken was still Digimon Kaiser, and their huge amounts Ho Yay, after Ken joined the main group. In fact, on Archive of Our Own the pairing outranks all others from the whole franchise.
An example comes from the voice actors surprisingly. As Bulma and Yamcha's seiyu reportedly didnt like the fact Bulma hooked with Vegeta in Dragon Ball Z, seeing as it threw away the growth the couple had throughout the early series and felt out of character for Yamcha to play the field.
Really Vegeta and Bulma only got together for the sake of plot and getting another Saiyan into the picture aka Trunks. Lampshaded in Dragon Ball: That Time I Got Reincarnated as Yamcha!, where the kid who is reincarnated as Yamcha loves Bulma but realizes that being her boyfriend and not training got Yamcha killed and secondly he has to let Vegeta get her for the sake of billions of people in the future.
A good chunk of the fanbase actually like Goku and Bulma together, since theyve had such strong connection from the start and Bulma becomes attracted to Goku seeing him as a grown man. But ultimately he ends up with Chi-Chi; lampshaded by Bulma herself where she reflects how lucky she couldve been to be his wife but understands she really missed the boat on that one.
One particularly painful example is Tien and Launch (particularly her mischievous blonde side) who have more fan support than most ships in the franchise but Launch was Put on a Bus (forever) despite all the ship teasing in Dragon Ball. Akira Toriyama said in a 2013 interview they do not end up together but remain good friends. It got especially annoying in Dragon Ball Super when some chick called Yurin was introduced as some weird Foe Yay for Tien all while Launchs existence was continuously ignored.
Some people also hate Videl Satan to the point where they ship Gohan with someone else, usually someone like filler character Lime or sideline nice-girl Erasa.
Similarly some fans detest Chi-Chi and ship Goku with Caulifa from Super.
A lot of fans of Dragon Ball GT thought Goten and Bra, as well as Trunks and Pan should eventually hook as way of uniting Goku and Vegetas families and ensuring the survival of the Saiyan-line on Earth.
Ho Yay side, a good chunk of fans actually prefer rivals Goku and Vegeta together rather being with their respective wives.
Episode 13 of Dog Days gives Cinque/Millhi as the Official Couple, but there's a lot of fanart out there for Cinque/Eclair.
Durarara!!: Despite the creator's insistence that the two will never get together Shizuo/Izaya continues to be the most popular ship in the fandom. While neither character officially hooks up with anyone, the novels imply that Shizuo has feelings for Vorona (even if he's not aware of it), while Izaya claims to love all humanity except Shizuo.
In Fafner in the Azure: Dead Aggressor, main characters Kazuki, Soushi, and Maya are supposed to be in a Love Triangle, with Soushi liking Maya who in turn is in love with an oblivious Kazuki. The thing is, Kazuki and Soushi have some great chemistry together, share a lot of very intimate moments, and Maya thinks that Kazuki would rather be with Soushi than with her. All of this has turned Kazuki/Soushi into an overwhelmingly popular pairing, to the point that shippy fanart about the two makes up about a third of all Fafner fanworks hosted on pixiv (for a reference, that's ten times as much fanart as Maya has, and she managed to avoid Die for Our Ship rather well). Before the sequel Exodus came out, Fafner's official website hosted a poll asking fans to choose their favorite moments in the franchise. Out of the five winners, four were scenes of Kazuki and Soushi bonding and showing affection for each other.
Fate/stay night: Although Rin is technically a love interest to Shirou Emiya, fans generally prefer to ship her with her Servant Archer instead, due to their snarky relationship which mixes elements of Mistress and Servant Boy and Lady and Knight together. Ironically, Archer is a version of Shirou Emiya from the future, albeit one who is heavily jaded by his experiences.
Fate/Apocrypha: Fans tend to find Jeanne/Sieg very dull, whether it's due to being too similar to the already lukewarm Shirou/Saber, their lack of chemistry, the apparent jump to love interests happening far too quickly, or just not liking Sieg. Because of this, people who like Sieg tend to prefer him with Astolfo, who is more popular, contrasts Sieg better, and has more evident chemistry. It also frees up Jeanne, who can end up with Mordred, Marie Antoinette, or her own Alter counterpart. This one even got some official acknowledgement in Learning with Manga, where Gudao watching the show immediately interprets the two as a couple, and even gets jealous over it.
Fruits Basket is a shipping goldmine! While many support the cannonical Kyo/Tohru, Yuki/Tohru and Kyo/Kagura complete the love triangle with a large fan base. On the yaoi side, Yuki/Kyo and Yuki/Hatsuharu are pretty popular too.
Interestingly enough, there was a pretty respectable contingent of Haru/Akito shippers... but only when Akito was thought to be a boy.
Roy/Riza ("Royai") of Fullmetal Alchemist seems to be of the "set it up as fan-preferred for extra credit when it becomes official" variety; many other charactersacknowledging it, and the mangaka herself needing to address why they don't happen. But the true Fan Preferred Couple of the series is Roy/Ed, which is unsurprisingly popular with slash fans (especially among fans of the first anime, where there was far less Royai build-up), even with Ed being in an Official Couple with Winry by the end of the manga/Brotherhood.
Overall, the whole issue of shipping is one of the big divides between fans of the 2003 anime and those of the manga/Brotherhood; fans of the latter overwhelmingly prefer the various Official Couples, whereas the former focused less on romance and had a more ambiguous ending, leaving fans to draw their own conclusions. (For example, part of the reason that Roy/Ed was so fan-preferred is that the first anime's Het shippers were fiercely divided over whether Ed belonged with Winry or Rose, who was a much more important character in the 2003 anime continuity.) However, overall, Roy/Ed remains the most popular ship when one crunches the numbers on fanfiction and fanart sites, especially in the Japanese fanbase.
Elricest (Alphonse and Edward) is far, far more popular with 2003 fans than in the manga-verse. The ending to the series, with them being on the other side of the Gate away from their friends and in turn from love interests, only helped.
Though shipping Edward with Winry was exceedingly popular for 2003 fans, it's also very common to pair Winry with Sheska. The same reasons above only made people ship it more, even some EdWin fans.
There is also a relatively small but determined faction which prefers to pair Winry with Alphonse. It's also a popular Ship Mate for Ed/Roy or Ed/Rose.
For those few fans who include Noah in their fanworks, she's usually shipped off with Alphonse. This leaves Ed open to date alter!Roy, alter!Winry, or Alfons.
Connected to it, as the two girls befriend, a lot of fans started to ship them with each other rather than Ryuuichi.
Quite a few Genshiken fans would love to see Madarame and Saki at least try to get together. Sure, Madarame seems to have a disadvantage compared to Kousaka in the looks department, but he and Saki seem to be a much better match when it comes to temperament. They also like to tease each other a bit too much for comfort.
Ghost Hunt has Naru/Mai and Monk/Ayako. Some fans also seem to like Masako and John together; an odd pairing given that the former only has eyes for Naru in canon and the latter is a Catholic Priest.
The Great Pretender fandom is heavily focused on the Makoto/Laurent ship, moreso than the ship teased Makoto/Abbie, and the formerly-canon-but-now-over Laurent/Dorothy. The two have a rather Ho Yay-laden relationship, with Laurent having a bad case of No Sense of Personal Space where Makoto is concerned, his constant teasing, and calling him by the Affectionate Nickname "Edamame." There are hints in-series that this is intentional—when Laurent playfully flirts with his associate Cynthia (and informs her he's doing so), she responds, "I thought Edamame was your favorite?" While it's left ambiguous whether she's referencing a genuine attraction on Laurent's part or just teasing him about his favoritism, fans latched on to the former interpretation.
While the official pairing in Guilty Crown is quite obviously Shu and Inori, many fans actually consider Ayase or Hare as better romantic partners.
''Haikyuu!!: Many fans like the idea of Kanoka getting together with her crush Tanaka who at the very least supports and admires her. Even after Tanaka marries Shimizu, some still prefer him to be with Kanoka.
Tsukushi was originally supposed to end up with Rui in Boys over Flowers but Tsukasa/Tsukushi became so popular with fans it became the Official Couple, which is ironic because after the manga finished, Rui/Tsukushi became the Fan-Preferred Couple because a lot of people thought Tsukasa became an incredible jerkass at times who kept upsetting Tsukushi while Rui gradually became a much more friendly and warm young man who was always there for Tsukushi.
The most popular Hellsing couples are Alucard/Integra, Alucard/Seras, Pip/Seras and Alucard/Walter (the young or Dark Walter versions...which is ironic since canonically Alucard refers to Walter's natural, elderly body as being trillions of times more beautiful than his artificially youthened one).
Walter/Girlycard. Sometimes, the fans make Alucard take his girl form (aka Girlycard) in Alucard/Walter stories.
Despite him being an Official Couple with Rias Gremory for around 10 volumes, the protagonist of High School Dx D, Issei Hyodo, gets shipped more often with Akeno Himejima than with Rias. This is partly due to their personalities being more or less in harmony: Issei is a Lovable Sex Maniac with an eternal fixation for the female breasts, while Akeno is a tease-happysadomasochist - as well as a Yamato Nadeshiko, and also has the largest recorded rack among all the girls in the series with an astounding 40". This is further helped by Akeno being the first girl in the harem that Issei goes out on a date with. Something worth noting is the near-total lack of any Ship-to-Ship Combat for this one - according to both Word of God and the text, Issei/Akeno is just as canon as Issei/Rias, and Akeno gets a kick out of being the "mistress".
Many Hot Gimmick fans prefer Hatsumi to have ended up with her (adopted) brother Shinogu rather than Ryoki, given Ryoki's treatment of Hatsumi. And in the novel, Hatsumi actually does end up with Shinogu.
Inuyasha: A vast majority of the fandom is very evenly split between pairing Sesshomaru with either Rin or Kagome, ignoring his canonical Implied Love Interest status with Kagura. The reason for the even split is because Rin is eight years old and (though he doesn't directly admit it because that would mean admitting he actually cares about a human) Sesshomaru's adopted daughter, and therefore causes controversial Wife Husbandry support/squick debates. Kagome's status as the Girl Next Door character makes her an extremely seductive, and less controversial, Wish Fulfillment alternative for shipping fans.
Due to the nature ofJoJo's Bizarre Adventure, fans tend to prefer the JoJos with their Heterosexual Life Partners or Rivals instead of their canon love interests (if they even have one). The top picks seem to be Joseph/Caesar, Jotaro/Kakyoin, Josuke/Okuyasu (in western countries), Josuke/Rohan (in eastern countries), Giorno/Mista, Jolyne/Ermes, and Johnny/Gyro. Jonathan/Erina and Josuke/Yasuho are pretty much the only canon protagonist romances to stick. Of the non-JoJo related couples, Bruno/Trish and Diego/Hot Pants prove to be quite popular.
Shizuku and Natsuru in Kämpfer are essentially this in the eyes of the fans, who love seeing Shizuku trolling the hell out of Natsuru. The Official Couple according to the Light Novel is Natsuru and Akane, while the anime opted for the "everyone wins" route. The manga has Shizuku winning.
Kiss Him, Not Me: For those who like yuri, Serinuma/Nishina is probably the preferred ship, helped by the fact that Nishina is legitimately part of Serinuma's harem and she shares a lot of good points with Mutsumi.
Little Witch Academia: Despite some hinting towards Akko/Andrew, fans (and even some of the crew) would much rather have Akko/Diana as the end game, given the large amount of development their relationship had over Akko's relationship with Andrew. Enough so that Andrew's original intent as a canonical love interest was vetoed early in development; aforementioned hintings being a compromise/reference to his initial purpose. Not enough, however, to make the preferred pairing canonical, as they've gone on record saying it will never leave the realm of fanworks.
Lucky Star: There are quite a few fans who choose to believe that Ayano isn't dating Misao's unseen older brother, but rather, this is a euphemism to cover up her relationship with Misao herself.
There's the popular pairing of Ruri/Akito in Martian Successor Nadesico. This is also kind of aided by the fact that their seiyuu, Omi Minami and Yuji Ueda, are married in real life.
Medaka Box has Zenkichi/Emukae. Medaka/Kumagawa definitely seem to be fairly popular as well, compared to the canonical affection Zenkichi has for Medaka which seems to be reciprocated as of Chapter 140.
Many fans of Midori Days seem to prefer Ayase/Seiji more than the official couple.
The amount of Domon/Allenby shipping in Mobile Fighter G Gundam is rather amazing considering that this show came before the series that allegedly attracted all the stereotypical shippers to the franchise. Proof that Love Triangles can survive and thrive even in a fairly straightforward shounen kung-fu-with-giant-robots show. The fact that Allenby herself is a Shipper on Deck for Domon/Rain, and the one who convinces Domon to tell Rain how he feels, doesn't seem to have gotten in the way.
The manga adaptation played up Allenby and Domon's teasing; the artist made it clear in an interview that he preferred Allenby to Rain.
A lot of Gundam SEED and Gundam SEED Destiny fans still scoff at the official pairings and think Kira/Flay, Athrun/Cagalli and Shinn/Stellar are a lot better. The fact that Athrun/Cagalli were broken up in canon seemingly because of a real-life feud between the head writer and Cagalli's seiyuu has, if anything, made fans ship it even harder out of defiance.
My Hero Academia: All Might/Inko became a popular pairing after Chapter 97 after the former admitted he admired her, not only for her resemblance to his deceased mentor, but her personality too. Despite Inko being canonically still married to Izuku's father, several fans prefer to simply ignore this fact either by portraying All Might as Midoriya's father or Inko as being divorced (helped by said father being The Ghost).
Naruto/Sasuke has been going strong ever since their Accidental Kiss in Chapter 3. Naruto/Sasuke is the most popular pairing on FanFiction.net and ArchiveOfOurOwn.org. It helps that the anime showcases a lot of rather... romantic moments between them, either in Filler or the openings and endings. You can see the Naruto Ho Yay page for more details, where they have an entire folder.
While Sakura does marry Sasuke and have his child, a good many fans still prefer her with Rock Lee, Sai and aforementioned Naruto simply because Sasuke treats her so goddamn terribly. Kishimoto did acknowledge the flaws in Sakuras love for Sasuke, but stated she would be a terrible person if she moved on from her Single-Target Sexuality—though given shes labeled as The Scrappy by a majority of fans becauseof her obsession with Sasuke, having her move on like Ino (who was also very attracted to Sasuke) did when she married Sai wouldve likely been a point in Sakuras favour. Especially to the unforgiving fandom.
Tsunade and Jiraiya, before the latter died. The latter's love for the former is canonical but unrequited, both before she met Dan, her canonical boyfriend, and after Dan died. Though with that said Tsunade did say to Jiraiya she mightve give him a chance then he dies soon after while Tsunade hides her tears and remains single forever.
Going by amount of fan fics and communities, it looks like Haruhi/Kyouya counts as this. Maybe it's Kyouya's more ominous and even humorously evil personality in contrast to the sweet but dumb and clingy Tamaki or maybe it's fans just plain not wanting the independent Haruhi to end up with a Manchild like its a sitcom. Kyouya respects her intelligence and independent nature while Haruhi can match wits with Kyouya- seeing through his lies and cool facade to the good-natured man afraid of being seen as soft underneath.
Haruhi/Hikaru also counts across more avenues of fandom. While both the twins care for Haruhi, it is the more-clueless Hikaru that must be pushed into recognizing his feelings by his brother that gets the most time with Haruhi. The two get entire episodes together, showcasing their quirky dynamic of the unflappable, Only Sane Man Haruhi with the rich but savvy Hikaru. Helping matters is that Haruhi is the only person ever able to tell the twins apart, allowing the two to feel like their own persons for the first time in their lives; something that they have always wanted but dreaded at the same time.
Hikaru/Kaoru is the third most popular pairing on fanfiction.net. Not surprising, given how incredibly close to two are and just by the virtue of their club gimmick hyping up their relationship so much.
Though Honey gets a female love interest in the manga, most of the fans still prefer him with Mori.
Some fans of Paprika have lots of trouble accepting that Chiba loves Tokita, and would rather have had her end up with Konakawa. This ignores how the fake ending with Konakawa and Chiba kissing in the sunset is supposed to be making fun of trite, cliché movie endings, which implies that pairing them together would have made for a really, really bland and predictable ship.
NaoandReika, who are childhood friends, are already proving to be quite a popular couple as well, and have several hints scattered around. The "Nissan combo", Nao and Akane, just about rival them in popularity.
Also, Joker and Reika, despite the fact that the two times they've actually interacted, in episode 23 and 43, they were fighting against each other, with Joker being as creepy as he always was.
Project K has Kuroh/Shiro, and Mikoto/Munakata to the point where it's rare to see them shipped with anyone else. Though the best example in the series is probably the Fushimi/Yata ship that has both very overwhelming and enthusiastic support from both the Japanese and western fandoms. The creators are very aware of the fan preferred couples and often pander to them.
Puella Magi Madoka Magica: Though it doesn't compare to the juggernaut of Kyouko/Sayaka, Hitomi's most popular pairing is not with her canon paramour, Kyousuke, but instead with Sayaka. Technically, Kyousuke/Hitomi is more common, but that's only because it gets Kyousuke out of the way in Kyouko/Sayaka; the pairing itself has few actual fans. If Hitomi is a main character, most of the time, she'll be paired up with Sayaka. This is only helped along by the PSP game directly suggesting that Hitomi is interested in other girls, despite her protestations to the contrary.
In Ranma ½: Ryoga Hibiki is almost always paired with Ukyo Kunoji, rather than their respective canon suitors, Akari Unyuu and Konatsu the kunoichi, due to the fact that most of their "romance" felt like a tacked-on Last-Minute Hookup with no development.
A huge majority of the fandom ships Tsuna with Hibari rather than his two canon female interests. It has to do with Hibari's fixation with Tsuna's growing strength, obsessively challenging him to fights (which Tsuna always declines), his suggestive catchphrasenote I'll bite you to death, and him being the stoic Bishounen to Tsuna's naïve personality has fans shipping both by droves. It helps that Future Hibari actually respect's Tsuna's leadership in the Future Arc, which made the shippers ship them harder.
Sidekicks Yamamoto and Gokudera are the most popular ship among American fans, as they like to turn Gokudera into a Tsundere for Yamamoto while kicking Tsuna out of the narrative or ship him with Hibari. Some keep Gokudera's obsession with becoming Tsuna's right-hand man and give all the romantic teases to Yamamoto.
As for the het couple fans, a lot of rare male fans find Tsuna and Harus relationship much more enjoyable due to Harus unique personality than Tsuna and Kyokos stereotypical puppy love Token Romance.
Many of the fans who watched the Rurouni Kenshin prequel OVATsuiokuhen/Trust and Betrayal or read the corresponding Remembrance arc in the manga came to prefer his lost love, Tomoe, over his Second Love, Kaoru, in spite of the teeny-tiny problem of Tomoe being dead by the time Kenshin meets Kaoru.
Many fans find the more emotionally expressive pop idol Seiya Kou from the Stars season to be a much better match than the more subdued Mamoru because Usagi and Seiya's personalities mesh well together. The series conveniently keeps Usagi painfully oblivious to Seiya's feelings up until the end of the series. This is also not helped by the manga having Seiya love Usagi from afar (and even forge correspondence from Mamoru since Usagi was still in denial over him dying in front of her) and the anime actually using her as a Replacement Goldfish when Mamoru was Put on a Bus.
Many fans find the more subdued JunKudou to be much better to the depressive Nozomu than the cheerful Kafuka because Nozomu and Kudou's personalities mesh well together, despite rarely interacting in-series. It looks like the author picked up on it too, with Kudou starting to appear much more, coincidentally ramping up the Ho Yay between him and Nozomu. He even started appearing more than some of the girls. Played for laughs, of course, until the author decided to Throw the Dog a Bone to the fans, by revealing that Kudou has feelings for Nozomu because of the blood transfusion he received from Kafuka, thus becoming part of Nozomu's harem in the end. More specifically, it's implied Kafuka was possessing him when she married/consummated the relationship with Nozomu.
Despite the series being extremely obvious about pairing Nozomu/Kafuka, it wasn't a very popular pairing, because of Kafuka being a Manic Pixie Dream Girl to him, something that fans consider rather cliche. The popularity boosted upon the revelation that Kafuka was Dead All Along.
While Ken and Jun officially got together at the end of the third series of Science Ninja Team Gatchaman -Gatchaman Fighter-, there is part of the fanbase that prefers that Jun be with Joe instead, feeling that Joe is more interesting of a love interest and pointing to various moments in Gatchaman II where the two seemed closer than Ken and Jun had. This extends to the only (at time) English adaptation of the same sequel, where the dub writers seemed to be pushing Joe and "Kelly" more as a possible couple.
Some Sekai-ichi Hatsukoi fans would prefer Chiaki with Yanase than Hatori. This has to do with Hatori brutally raping Chiaki and episode 16 that pulled everyone's heartstrings.
For the Sgt. Frog fanbase, you're more likely to find fanart of Giroro with Natsumi rather than her canon crush, Saburo. There's also as much Natsumi/Koyuki fanart.
The most popular pairing in Slayers fandom used to be Lina/Zelgadis, given that both are level-headed and intelligent (despite the fact that Zelgadis cannot stand Lina at times), as opposed to the canon Lina/Gourry. Nowadays, it has a rather small following. This might have something to do with Amelia becoming less hated over the years, partly due to character development. Other official works have noted this - the Light Novel series artist now draws Zelgadis and Amelia together, and several manga adaptations, namely the manga version of the fifth anime season, has a massive Ship Tease in regards to them.
Soul and Maka from Soul Eater, though the same can be said for all of the meisters and their weapon partners. Kid/Crona is also very popular, especially on deviantART. Although meister/weapon pairings are very popular, Soul/Maka seems to be the biggest faction, with at least three separate deviantART fangroups.
There's also a significant faction of Kid/Maka, Kid/Soul, Maka/Crona, and Stein/Spirit supporters that should not be overlooked.
Shuuichi, Kumiko's official love interest, is largely treated as a non-entity by fans. Until proven otherwise the anime is unofficially a Yuri Genre series themed around high school band club members. The original light novel is more direct about Shuuichi and Kumiko as the Official Couple, while the anime emphasizes Kumiko's budding friendship with Reina and has incredibly heavy Ho Yay between them, treating Shuuichi like a platonic childhood friend. Word of God in the between-seasons period was somewhat rudely dismissive of Kumiko/Reina (despite the obvious baiting in the anime). Just to make things even more confusing, Kumiko seemingly confesses to a different female band member at the end of the second season, but this may also turn out to be misleading.
Sugata/Takuto in Star Driver. Even amongst the actual characters. Takuto/Mizuno is also liked in some circles.
Many fans Strawberry 100% wish that Junpei picked either Aya or Satsuki over the actual winner, Tsukasa.
Strawberry Panic! fans will often hate Amane for two things: taking away their beloved Hikari/Yaya Coupling and being a Bifauxnen. It doesn't help that many viewers, and several reviewers, who weren't even in a Shipping mindset, found the Hikari/Amane romance subplot to be bland and forgettable.
Tantei Team KZ Jiken Note: When Sunahara appeared in episode 5 (animating part of the fourth novel The Egg Hamburg Steak Knows), the western viewers immediately picked up Sunahara X Aya and prefer it over the "default" Wakatake X Aya, reasoning that a Nice Guy like Sunahara is a better choice to introverted Aya than the Hot-Blooded, impulsive, and occasionally jerkass Wakatake. Although later on in the anime the direction does turn to Sunahara's side; Aya and Sunahara has mutually confessed (despite still Star Crossed), while between her and Wakatake it's more of a case of an ambiguous Just Friends plus mutual Green Eyeing.
Tenchi Muyo!: Kiyone and Tenchi is extremely popular with fans too, for the same "overtly normal or at least sane" reason as Sasami without the incest and pedophilia problems. Unfortunately Kiyone appeared only in spinoff media, Tenchi Universe hinted heavily towards Tenchi liking Ryoko, Tenchi in Tokyo ended ambiguously without a Word of God, and, most importantly, Kiyone was the only girl, perhaps in the entire franchise, who showed no romantic interest in Tenchi, which just made fans want it more.
Surprisingly, even with all those ship tease between Ako and Shou, the most popular ship of Thriller Restaurant is Anko/the Garçon. It must has something to do with the ED and the implication that they really have met before.
Toriko: After the time-skip, Toriko is engaged to Rin and ends up marrying her at the end of the series. However, the fact that Rin has very little relevance to the plot and that Toriko and Komatsu are much, much closer to each other with a hell lot more chemistry (in fact, Komatsu is Torikos chef partner, not Rin, and he is the Deuteragonist with the second most important role in the plot) have led most of the fans to ignore Toriko x Rin official status and keep on shipping Toriko x Komatsu. It doesnt help that even after being engaged to Rin, Toriko still spends much more time thinking about Komatsu than spending a panel to think of his fiance; and at the end of the series, he leaves Rin at home to go to space with Komatsu to find ingredients, just the two of them alone. Most fans agree that Toriko x Komatsu would have been canon in a heartbeat had Komatsu been a woman and not a man.
×××HOLiC has the dynamic duo of Doumeki and Watanuki as the, without a doubt, most popular pairing in the fandom. It is very rare to find anyone who ships Watanuki with anyone other than Doumeki, despite the fact Watanuki 1) never fully gets over his unreasonable distaste for Doumeki, 2) has a massive crush on his classmate Himawari and 3) by the end, has at least three other potential love interests.
Rein and Eclipse from Twin Princess of Wonder Planet were more popular (in fact, the most popular pairing) in Japan than the Official Couple Fine and Eclipse, at least, before the second installment began. Even Mayuki Anan, the artist of the manga adaptation, seemed to prefer them, as Rein and Eclipse got more Ship Tease than any other pairing.
While the canon Keith/Allura pairing has a LOT of fans, an almost equal number of Voltron fans like to pair Allura with Lotor, in part because of Lotor's Draco in Leather Pants vibes, and in part of scrub off some of the Purity Sue aspects of Allura. It should also be noted that a small but vocal minority would prefer Lance be with Allura.
Takatsuki/Chiba is the most popular pairing, what with their large amounts of Foe Yaywhich diminishes just into Ship Tease over time once they become best friends again. In the end however Chiba dated Fumiya while Takatsuki ends up with an unrequited crush on Nitori.
Takatsuki/Nitori is quite popular, which is expected from opposite gender major characters. Nitori liked Takatsuki early on but it was unrequited. This is reversed in the end as Nitori has a long-time girlfriend while Takatsuki realizes her feelings for Nitori, which are now unrequited after so many years.
Doi/Nitori is pretty popular amongst anime fans but not manga fans.
J.J./Yurio was this for a bit even after the introduction of J.J.'s girlfriend Isabella, who shared his arrogance. It died down both when Isabella showed her sweeter side (supporting J.J. after his disastrous GPF short program) and when Otabek was introduced and overtook J.J. as the fandom's preferred Yurio love interest.
Christophe is shown to be close with a nameless man who may or may not be his boyfriend, but their relationship is rarely found in fanfiction other than as a secondary couple. When Christophe is the focus, it's way more common for fans to pair him with Phichit or other major characters.
Ai Mizuno and Junko Konno exploded in popularity as a paring, and is easily the largest ship tag related to the series on Pixiv. Once they became popular together, a lot of official art with the two was released. Season 2 certainly plays into the interest of them being together, and episode 4 is pretty much nothing but pandering to their relationship.