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.
Serpico/Farnese is an incredibly popular pairing within the fandom, thanks to their Lady and Knight dynamic; with Farnese starting as a Dark Lady and then becoming a Bright Lady and Serpico remaining a mostly White Knight to her through. The devotion to the ship is so strong that not even Farnese being engaged to the popular Roderick or even Farnese and Serpico being half-siblings can sway fans.
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.
Uryuu/Orihime took off in the Soul Society arc once they teamed up for their journey through the Seireitei, liberally aided by Innocent Fanservice Girl jokes to embarrass The Stoic Uryuu. This continues into the Arrancar Arc, especially after Ichigo leaves Orihime in Uryuu's care while he fights Ulquiorra. Orihime's canonical Love Confession to an unconscious Ichigo was not popular with these shippers, although Orihime never expressed any romantic interested in Uryuu before that either.
Pairing Uryuu up with Nemu was also quite popular, especially as her father is Uryuu's Arch-Enemy and yet Nemu still treats Uryuu kindly and Uryuu himself seems concerned for her welfare and is horrified by Mayuri's treatment of her.
The Arrancar Arc kicked off an extremely controversial but popular Ulquiorra/Orihime ship. As her kidnapper and captor, Ulquiorra's scenes with her are interpreted by shippers as Mind Game Ship due to the canon plot line being based on using Orihime's gentleness to teach Evil Cannot Comprehend Good Ulquiorra the value of human emotion and compassion.
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.
Zaraki/Unohana was a fairly popular crackship, until it actually became somewhat canon. Then Unohana died.
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 timeskip and and 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.
If the forums of various sites are to be believed, then Akira/Rion is by far the most popular pairing in Cage of Eden, and for good reason, due to their willingness to protect and take care of each other, no matter what happens. Akira/Mami seems to be gaining popularity quickly, though.
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).
In The Cat Returns, Haru/Baron is one of the most impossible couples to actually get together (except through very powerful magic, more so than the Cat Kingdom's cat turning abilities), with Baron being a foot-high, half cat living statue and Haru being a fully human, normal height school girl. Doesn't stop the fans from shipping 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.
D.Gray-Man: Although by far one of the most popular couples, the mind-numbingly obvious pairing of Allen and Lenalee has accumulated a fair amount of haters. Most of the remaining in the fandom are proud Yullen (Kanda/Allen) fans because of a "hate/love" appeal.
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.
Dangan Ronpa 3 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.
Continuing from the firsttwo games, Makoto/Kyoko and Hajime/Chiaki were widely rooted for by the fandom, thanks to the piles of Ship Tease and Implied Love Interest vibes the anime added on. The fandom outright rioted when both girls were apparently killed off (Kyoko got better; Chiaki didn't). Izuru/Chiaki also started becoming popular in its own right, although that's a weird case as Izuru has Hajime's body, but a different personality.
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.
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.
Adventure and 02:
In a rather infamous example of Relationship Writing Fumble, Taichi and Sora became a vastly more popular couple than the canonically-intended couple of Yamato and Sora; show director Hiroyuki Kakudou claims to have explicitly set up clues foreshadowing that Yamato and Sora would eventually be married, but almost everyone else involved appeared to ship Sora with Taichi insteadnote Including the Voice Actors — Yuuto Kazama and Mayumi Yamaguchi, respectively the voices for Yamato and Gabumon, had expected Sora and Taichi to end up together — and secondary director Mamoru Hosoda, who directed Our War Game.. 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. Especially notable in the American dub, which latched onto the Taichi-Sora pairing early. Given discontent fans, divorce fics ensue.
Takeru and Hikari (Taichi and Yamato's younger siblings) 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.
Koushiro/Mimi is one of the most popular ships in Japan, often going toe-to-toe with Takeru/Hikari (In the West, it's not as popular as Yamato/Mimi or Jyou/Mimi). Must have something to do with Opposites Attract. It seems the writers have caught on as well, since in tri. Koushiro now develops an explicit crush on Mimi, and they share plenty of Ship Tease with each other.
Mimi is also frequently paired up with Joe by the western fanbase, not at all hurt by the fact that some of the dub writers shipped it too and added some cute little Ship Teases between them.
While Ken and Miyako wound up married in the finale (a Development Gag based on the fact that their Voice Actresses got along so well), it's not uncommon to find them shipped with other people rather than each other, since they have very little in-show support.
Zenjirou has a crush on Nene, and despite teasings for Taiki/Akari and Kiriha/Nene in Hunters, Kiriha/Taiki and Taiki/Nene are much more popular.
On the actual Digimon (as in, the creatures) side of things, lots of people tend to ship in the Adventure/02 canon either Veemon/Gatomon, Patamon/Gatomon or Wizardmon/Gatomon, based on the opposites or similarities the formers have (and their connections to the Daisuke/Hikari and Takeru/Hikari pairings) or the deep friendship the latter had. Meanwhile, in the Tamers section of the fandom, people seem overly fond of the Renamon/Impmon ship, based on their chemistry and Ship Tease moments. Some people have even come to ship theirMegaforms.
Episode 13 of Dog Days gives Cinque/Millhi as the Official Couple, but there's a lot of fanart out there for Cinque/Eclair.
Though they're only hinted in Eyeshield 21, Sena/Suzuna and Hiruma/Mamori do have their own followings.
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: The series allows each of the three love interests an equal shot to star in the spotlight and to hook up with the main character. But because the story is so intertwined with the girl at the route’s center, judging her relationship’s own merits with Shirou is tricky because fans can let their personal liking for the girl or her route influence their opinion of the ship. On top of this, all the routes are dictated to be just as canon as the others, leaving which ship counts as the fan-preferred one down to which of the main character’s ships is the most popular.
The general trend seems to favor Shirou/Rin of Unlimited Blade Works. Storywise, the middle route blends the heroic optimism and cynical deconstruction of the two other routes, providing a little something for everyone. Rin is generally considered the “best girl” of the three- for fans and for the leading man himself, thanks to her iconic portrayal which defined the modern Tsundere. Unlike the other girls, Rin is a fellow Master who works with Shirou as partners, allowing their romance to bloom on equal terms. Her take-charge attitude guides the two through the war and pushes the normally passive Shirou to stand up for himself while his compassionate nature pushes Rin to follow her conscience and do the right thing.
Thanks to the Fate route's Vanilla Protagonist portrayal of Shirou (as well as his rather sexist treatment of Saber), Gilgamesh's cut-throat courtship of Saber has drawn more fans to it than the route's actual romance. Gilgamesh believes all treasures in the world are his, including Saber; in return, she fights him and spurns him at every turn, which only makes Gilgamesh want her all the more. At no point does Saber develop feelings for Gilgamesh as is so common with this trope; remaining the strong-willed and proud knight Gilgamesh came to love (in his own way) in all routes. And while Gilgamesh may not respect Saber as a woman, he does acknowledge her as an equal (just not one whose opinions will stop him), and considering his ego, this is saying a lot.
Fate/Zero: While popular before, Gilgamesh/Saber rose to definite top status with the prequel showing them interacting as relative equals. Though he, and by proxy the ship, is still twisted, Gilgamesh is much more humane and sane in this versionnote as it turns out, the Grail did in fact corrupt Gilgamesh, which is the reason he is so unhinged in the sequel and even gets a few Pet the Dog moments. Gilgamesh tortures others for his own amusement but also saves Saber from Berserker and spares Waver for his loyalty to Rider. In general, Gilgamesh shows respect and affability to his fellow kings- especially through defending a shaken Saber’s ideals from the disapproving Iskander. As such, the anime makes the pairing into a potentially plausible but still outright Mind Game Ship.
Lancer/Saber is a decent close-second, especially for those who prefer a more healthy and balanced ship. Both are chivalrous knights who respect each others ideals and immediately bond on the battlefield to the point where they come to each other's aid. It’s even referenced in one of the OV As- Lancer imagines holding hands with Saber as they frolic in a field of flowers.
Rider/Waver is so popular that it is virtually canon given how many Ship Tease moments it gets. Wordof God states they most likely replenished prana ''that'' way and one of Rider's followers seen in his Reality Marble bears a striking resemblance to an adult Wavernote due to the Throne of Heroes existing outside of time, this stranger could actually be Waver himself. There was even an April Fool's Day manga about an otaku Rider and a female Waver falling in love.
In the Free! fandom, judging by the nigh-constant Ship-to-Ship Combat between the two pairings' supporters, fan preference seems to be split between Rin/Haruka and Makoto/Haruka. Of course, Nagisa/Rei may transcend both sheerly because they work as Ship Mates to any combination of main-character ships in the series.
Fruits Basket is a shipping goldmine! While many support the canical 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.
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 original 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 her 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.
Many fans prefer to pair Miaka with Tasuki instead of Tamahome.
Suboshi is far more popular a love interest for Yui than Yui's canon boyfriend, Tetsuya.
Rein and Eclipse from Fushigiboshino Futago Hime 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.
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.
Gintama has so far no Official Couples, and the chances of there being any are slim, but this has not daunted the shippers in any way. Okita/Kagura, due to the Foe Yay and Belligerent Sexual Tension between them, are ardently shipped together. A close second would be Gintoki/Tsukuyo, especially after the Ship Teasy Red Spider arc. Yaoi couples such as Gintoki/Hijikata and Hijikata/Okita are also hugely popular due to a large part of the fanbase consisting of Yaoi Fangirls.
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!!, like a lot of sports series, has a large shipping community that predominantly supports male/male ships, with almost every major character being in at least one super popular one. Among the largest are Kageyama/Hinata, Daichi/Sugawara, Oikawa/Iwaizumi, Bokuto/Akaashi, Tsukishima/Yamaguchi, Asahi/Nishinoya, and Kuroo/Kenma.
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.
A lot of people who have read the Haruhi Suzumiya novels are of the opinion that Kyon/Yuki is the perfect couple. This can be attributed to the 4th novel, Disappearance, which focuses majorly on Yuki and Kyon, as well as the fact that Haruhi tends to go Out of Focus, while Yuki becomes more focused on, all combined with an utter lack of any major Haruhi/Kyon hints. The fact that the author himself has said Yuki is his favourite character may also help. It may also help that Yuki is beloved by an enormous portion of the fandom, individuals at worst not expressing any interest in her, while Haruhi, though popular as well, has acquired a significant force of haters due to the more abrasive and violent portions of her personality. It also doesn't hurt that there's an entire AU spinoff devoted to this ship.
In the Hayate the Combat Butler fandom the majority of fans seem to be divided between Hayate/Hinagiku and Hayate/Athena. While Hinagiku continues to completely overshadow the entire cast in terms of popularity, Athena is a firm second and discussions on the forums can be split pretty evenly. Notably neither of the girls is one of the main heroines, those being Nagi and Maria who have more supporters than the other 'auxiliary' pairings but not nearly enough to compete for fan-favor.
Wataru/Saki is also incredibly popular among the fandom despite Wataru being interested in Isumi and Sonia having an obvious interest in him. Recently in the manga it seems that the Wataru/Saki shippers might have won after all, as Wataru confessed to Isumi that he loved her and has since dropped out of Hakuou to focus on his business with Saki.
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".
The fandom is split on who Keiichi should be with, with all of the girls claiming a share of fans. Rena and Mion being the most popular, with Mion having more fanworks than Rena in the end (early on it was the other way around).
The most popular ship for Rika is her and Satoko together. It is far more popular than Rika/Hanyuu, Satoko/Hanyuu, or Rika/Keiichi.
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.
If the sheer amount of fan arts on likes of Pixiv are anything to go by, Shibuya Rin and the Producer pairing is the most popular pairing in THE iDOLM@STER: Cinderella Girls. This is probably helped by the fact that those two are often shown onscreen together, more frequently than any other characters in the anime.
Any talk of shipping with fans of Infinite Stratos will more or less revolve around pairing Ichika with Charlotte, due to her being the least likely to go angry at him among the other girls pining for him. The end result: she achieves Breakout Character status, by becoming the first to have her own spin-off manga. And that is not even counting the fact that the ending for the said spin-off has been declared Better Than Canon.
Due to how incredibly Adorkable Laura is after her defrosting, many fans add her into the Ichika/Char pairing as an OT3.
Izetta: The Last Witch: People were already pairing Izetta with Princess Finé even before the series began airing due to the Ho Yay promotional artwork. Those feelings intensified after the series began airing.
Within the Kashimashi: Girl Meets Girl fandom it's extremely rare to see someone who ships Hazumu and Yasuna. This is despite, or maybe because, she was the girl Hazumu was going after for most of the series. The shipping was so noticeable that an anime OVA came out that killed the Hazumu/Yasuna ship with a flimsy excuse, to get Hazumu and Tomaritogether. It has a mild excuse in the anime, where the ending before the OVA does have aspects of Ass Pull. It's also worth noting that the manga did have Hazumu end up with Tomari at the end. The anime came out before the manga ended, though, so it's possible that the manga's ending was influenced to some extent by the popularity of Hazumu/Tomari.
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 according to the Light Novel is Natsuru and Akane, while the anime opted for the "everyone wins" route.
Kiss Him, Not Me: The series has a rather unfortunate plot involving a girl, Kae Serinuma, who starts being romantically pursued by four boys the moment she loses weight. Three of these boys did not care much or at all for her when she was fat; but the fourth boy, Mutsumi, was very kind to her, already seemed to have feelings for her before the weight loss, was the only one to recognize her after it, and does not care that she has socially unacceptable hobbies. So, a lot of readers immediately latched onto Serinuma/Mutsumi as the ideal ship of the series.
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.
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.
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.
Many Lucky Star fans like to ship Konata and Kagami together, and there have been some slightShip Teases, mainly on Kagami's part.
Magical Girl Lyrical Nanoha is infamous for its Ship Tease — sometimes metric tons of it — for couples that are not official at all. And that means basically all potential pairings, since there's exactly one Official Couple in canon to date... an off-screen hookup between a member of the supporting cast and a glorified extra. The fans have responded with Fan Preferred Pairings for most of the main cast, particularly Nanoha/Fate (which later got promoted to official status), Suzuka/Arisa, Subaru/Teana, Caro/Erio/Lutecia, and Vivio/Einheart. Hayate is a special case, with Hayate/Vita, Hayate/Reinforce and Hayate/Harem being about equally popular, often with the same people.
Mahou Sensei Negima! began with the daunting task of giving the male lead an entire classroom of love interests, a whopping thirty-one girls, with more added as time went on. Eventually six women emerged as having the best chances of hooking up with Negi, and fandom was pretty evenly split among them. Then the series ended. Badly. Very, very badly. And ambiguously, with a "Where Are They Now?" Epilogue that covered everyone's lives except on this one issue; it did rule out six characters, but none of them were the main six. In the final chapters, Negi did say he might like someone, but he's ten-years-old, it's not really a sign of a final commitment. UQ Holder! reveals that the girl in question was Chisame, and they marry some time later. Whether or not this was a good choice is subject for heavy debate.
Not including Negi, the most popular ship is Konoka and Setsuna. The epilogue implied with all the subtlety of a brick to the face that they got married. The only way that people don't ship the two of them together is when they're shipping them together with Negi.
Natsuki/Shizuru is also overwhelmingly popular. There are more Natsuki/Shizuru fanfics in the Mai-HiME section of fanfiction.net than there are all other stories combined. They are a couple in Mai-Otome, but that's a different continuity.
Jack/Snow is surprisingly more popular than Jack/Pano (if only because of the Ghost Chess arc) on forum discussions.
On the Ho Yay/Foe Yay side, you have Ginta/Alviss, Phantom/Alviss and Rolan/Alviss with the first two being nearly tied.
Basically, disregarding OCs and self-inserts, the most popular ships seem to be Ginta X Alviss, Ginta X Phantom, Alviss X Phantom, or some combination thereof, though some might argue the Yaoi fans are an extremely vocal minority. As far as heterosexual pairings go, Ginta is almost exclusively shipped with Snow, and Dorothy is near-universally paired with Nanashi. Jack is either left alone or paired with Pano, or rare cases with Snow. Alviss is... Unsurprisingly almost never paired heterosexually, but in the rare instance he is, it's usually Belle.
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 On the Ho Yay side, the most popular pairing would be Midoriya/Todoroki, after the Sports Festival Arc due to Midoriya becoming a Warrior Therapist to help Todoroki deal with his Dark and Troubled Past. After that, Todoroki's life does a 180º change, becoming able to visit his mom in the hospital and working with his father (not forgiving him yet), after that and during the Stain Arc, it's show that they become friends and both hold each other in high regards. On the Het side, Midoriya/Uraraka (or Izu Ocha in short) is quite the popular pairing for the main characters, reinforced in canon both by Izuku's inital attraction to Ochako and by the growing feelings of Uraraka for Midoriya and her sparse moments of jealousy when he interacts with Mei Hatsume, another less popular one is Momo/Todoroki, stemming from their interactions in their test with Aizawa.
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.
Shikamaru is so frequently paired up with Temari by fans in Japan, the West, and pretty much anywhere the manga is known that many assume it is already canon, even though they haven't technically gone on a date, although Naruto incorrectly assumed they had when he saw them walking together just after the Time Skip, and another girl named Shiho has shown romantic interest in Shikamaru. The series does hint heavily at something being there—they keep getting Ship Teasehalf-invisible to the naked eye—and Word of God agrees there is something between them, but seems to suggest it's just not important enough for us to get to see it happen on-panel until the Distant Finale which came with a Relationship Upgrade for many couples. Much like the aforementioned Naruto and Hinata, Shikamaru and Temari are shown to be Happily Married with a son. Shikamaru's post-manga light novel also includes Shikamaru asking Temari out on a date.
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.
Prior to the release of the Boruto anime, people began shipping the Konoha 11's kids together. The most popular pairings were Boruto/Sarada, Inojin/Sarada, and Inojin/Himawari. The latter two didn't even interact in Boruto: Naruto the Movie, Naruto Gaiden, or the Distant Finale; however fans began shipping them anyway. This is due to Inojin's and Sarada's mothers being best friends, and the Yamanaka's being florists while "Himawari" means "sunflower." Inojin/Himawari actually got an episode dedicated to them in the Boruto anime, in which they share their passion for drawing and ends with Inojin calling Himawari "sensei". Mitsuki/Sarada also began picking up speed after the Boruto film.
In the manga, Sumire states that she likes Boruto outright.
Fans frequently pair Konohamaru with Hanabi, due to them being of a similar age despite never having interacted before... until the Boruto anime episode 50, in which they both get drunk and share their affection for Boruto as a thing in common.
One Piece has a few, despite No Hugging, No Kissing being heavily hinted at as the author's intent. The fandom heavily prefers pairing Luffy with Nami, citing a unique relationship between the two as evidence, as well as the fact that author Oda's wife apparently cosplays as her. On the Yaoi side, Luffy is often paired with Zoro, or Zoro with Sanji. Other fan-favored pairings include the sorta-obvious Usopp and Kaya, as well as Zoro and Robin.
Hikaru/Kaoru is the third most popular pairing on fanfiction.net, despite it being the least likely of all the pairings to become canon.
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.
Each of Ash's female companionsnote not countingBonnie have had their share of Ship Tease moments, and, thus, their share of supporters for his hand, mainly correlating to either when the fan first entered or which season was a fan's favorite. As of the end of Best Wishes, however, Mistyhad stood the test of time; though she was aided by external support during her tenurenote specifically, a minor Writer Revolt in Japan sneaking in the Ship Tease compounded by Dub Text in the translations, plus an added Love Song in the 2.B.A. Master CD,, and despite other pairingsnote some being FPCs in their own right, see below.
Ash/Serena became absurdly popular in a very low time period, there is so much Ship Tease it's not even funny. Just to get an idea, in less than two months the pairing thread on Serebii got over 20,000 replies (no other shipping thread even reached 10,000)! Not to mention the huge amount of Japanese fanart. Of course this is helped along by blatant ship teasing (at least from Serena's side of the equation) that makes Pokeshipping subtle in comparison. At the end of the XYZ season, the fans exploded with excitement when the impossible happened; Serena kisses Ash before she leaves.
Gary Oak is still the popular Gay Option for Ash, even after several potential challenges.
Giselle, a Character of the Day from the first season, is still a somewhat popular option due her being the first (and, so far, only) girl Ash showed clear attraction towards.
With Pokémon/Human fans it's either Latias, Pikachu, Mew, or Bayleef. Which usually involves Ash turning into a Pokémon or the Pokemon turning human.
As indicated above, the pairings involving Ash are just the tip of the iceberg, as there are Loads and Loads of Characters, leading to loads and loads of ships.
Jessie and James is quite popular: It also works as a side ship to just about any other couple because it doesn't "get in the way of anything." Neary two decades of no romantic progression has put a dent in the ship, compared to the late 90s and early 2000s; however, it still has a steady fanbase.
Ash's Mom (Delia)/Professor Oak had a strong following for a while, partly due to Oak acting as Ash's father figure most of the series, and partly due to their offscreen (and several onscreen) locations being in close proximity.
May and Drew, which qualifies due to their resolution being an aptMaybe Ever After. For the duration of May's time in the main cast, every single time Drew showed up the writers seemed to be challenging themselves to make the Ship Tease even more obvious than last time without actually outright stating their feelings.
Dawn and Zoey were notable for several Les Yay moments early on in Sinnoh.
Alain/Mairin is a huge one. People started shipping them from the moment their designs were revealed, and it only continued to steadily increase in popularity as the Mega Evolution specials went on, to the point where you'd have to scavenge the fandom to find someone who doesn't ship them. Following the end of the specials, fans are left hoping for a happy resolution after their heartbreaking last moments together.
Despite the pairing being painfully one-sided,note though there seemed to be some reciprocity in their brief scene together in Unova, at Oshawott's expense, Pikachu/Buneary has tons of followers.
Tracey and Misty's sister Daisy are often shipped together, often as a Ship Mate to Ash/Misty and Oak/Delia. The ship comes from a few episodes where they interact together.
Though Dawn and Paul hate each other and don't share any Ship Tease moment together, somehow, this pairing has a lot of followers.note One of the reasons this ship is so popular is because of that one scene before Ash and Paul's battle at the Sinnoh League, where not only does Paul actually open up to Dawn, but also has Dawn blush at one point.
Manga shippers tend to go for Red and Yellow. Some go for Red and Bluenote Green in America. Bluenote Green in America/Silver, Gold/Crystal, and Ruby/Sapphire teeter on the edge of canon, but can still be called this.
If fans don't accept the trio of Diamond/Pearl/Platinum as a given, they usually tend to prefer Diamond/Platinum, mostly because of Dia's obvious crush on the latter.
Contrary to the games, Black/White is a much more popular ship amongst Pokémon Special fans than N/White, whose game counterparts are the components of one of the most popular game ships in existence. Ironically, the one thing that had Special fans dropping the N/White like hot potatoes was the one thing that made their game counterparts so popular. Can you say, "FerrisWheel?". Black/White exploded even further in popularity thanks to the train scene and the infamous ending of the BW arc, leaving both N/Black and N/White in the dust.
Aside from the faction that chooses to see them as Like Brother and Sister, X/Y is also more-or-less unanimously supported by the fandom.
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 fans almost universally support the Ship Mates Madoka/Homura and Kyouko/Sayaka. For most of them, it's not even a question; Het Is Ew is in full effect (not that it matters, since the only plausible male option is Kyousuke, who is officially paired with Hitomi, making both of them unpopular for fueling Sayaka's depression), and official merchandise and material does nothing to slow the train. For comparison, fanfics pairing Sayaka with Kyousuke, who she canonically had feelings for: 8. Fanfics pairing Sayaka with Kyouko: 148. The Movie did a lot to help these ships along, directly confirming that Homura loves Madoka, and Sayaka has thoroughly gotten over Kyousuke while being willing to return from the dead to meet Kyouko again. It's at the point where most consider them to be a dual Official Couple, with fans of smaller ships like Kyouko/Mami or Homura/Sayaka naming their own ships the fan-preferred couples. Word of Saint Paul has been very kind to this interpretation.
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.
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/
In Japan the reason that the anime was shown out of order was because they wanted to introduce Shampoo earlier to boost ratings since she was the fan favorite fiancée in that country where Shampoo/Ranma was the most wanted pairing at the time.
Mizore/Kurumu ever since their on screen kiss. Tsukune/Inner Moka is also the most popular pairing of the Harem. Even moreso after the finale, in which Outer Moka gets absorbed into her and most of the Tsukune/Outer Moka shippers get absorbed into the Tsukune/Inner Moka ship too.
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 fact that Seiya is actually female is not addressed by the series, though 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 Love Interest 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.
School-Live! has almost no romance due to it being about a bunch of girls getting through a Zombie Apocalypse together. There is enough Les Yay to get shippers worked up though, however manga fans and anime fans tend to split into two groups: People who began with the anime often enjoy Kei/Miki and Kurumi/Rii due to the anime borderline making Kei Promoted to Love Interest and because Kurumi and Rii mix well. People who started with the manga are prone to either Yuki/Miki or Kurumi/Miki due to the amount of close moments they have in the manga.
A strong portion of the (Japanese) Seiyuu Ka fanbase ships Haruka/Hime while lesser portions ship Senri/Hime and Mizuki/Hime.
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.
Fuyuki/Momoka is rather popular too. The fact that it's the closest the series has to an Official Couple helps this.
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), and the issue became a Base Breaker. 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.
For Strike Witches fans as of late, it's been Perrine and Lucchini. Many of their interactions are rather amusing in terms that they're complete polar opposites,with Lucchini almost always teasing her, especially episode 10 of the second season, where they share tons of Ship Tease moments, including Lucchini hugging Perrine as she's scared, then later throwing a sword to Perrine to defeat a golem, which got fans curious on how well they work together.
Sword Art Online: While the Official Couple of Kirito/Asuna does have quite a bit of support, there are plenty of fans who have their own opinions on who the couples should be.
For Asuna, there are plenty of fans who ship her with Yuuki, mostly due to their chemistry and the fact they have a very obvious Romantic Two-Girl Friendship going on, which gets lampshaded at several points.
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.
Some fans of Tears to Tiara like to pair Arthur and Octavia together, since they're both noble warriors and swordsmen with Sad Pasts that involve their dead loved ones. And of course the fans were excited when they saw episode 10.
Aside from the age and incest hurdle, Sasami from Tenchi Muyo! is big with fans for being the most subdued and overtly normal — or at least sane — girl in the show (in very general terms). In fact, before The Great Crash, this page was called "Sasami Syndrome". Word of God has it that Sasami will marry Tenchi eventually. Because everyone else will, too. Even then, however, many fans feel that Sasami alone - or any of the girls - would be preferable to Status Quo Is God.
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.
In Tsubasa -RESERVoir CHRoNiCLE- Kurogane and Fai are the biggest non canon pairing due to the massive amounts of Ho Yay between them, and the fact that neither of them have any love interests. Some fans are desperately looking for Kurogane/Tomoyo hints though, which makes everyone else laugh sardonically because...well, everyone who is familiar with the Tomoyo of Cardcaptor Sakura knows why. Word of God has (admittedly rather begrudgingly) moved them up to a more official status.
Tsubasa's Sister series ×××HOLiC has the similar 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.
Vampire Knight has Zero/Yuuki and Kaname/Yuuki. Many fans also support the relationship between minor characters Senri and Rima.
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.
There is little to no romance in Yotsuba&! but Koiwai/Fuuka is easily the fan favorite. Rule 34 is generally frown upon when it comes to this series but they obviously exist, and probably 90% of them are on these two. It helps that any ship tease that exist in the manga at all are between these two.
From Yu-Gi-Oh!, Yugi/Yami Yugi, Jounouchi/Kaiba, and just about every combination of Bakura, Marik, Dark Bakura and/or Dark Marik. On the hetero side, Yami Yugi/Dark Magician Girl (or Atem/Mana), Shizuka/Kaiba, Isis/Kaiba, Mai/Yugi, and among others.
Puppyshipping (Jounouchi/Kaiba) is one of the biggest pairing in the whole fandom, despite the fact that the two are neither even remotely friendly nor actual rivals, treating each other with a fairly dismissive hatred. It mostly comes from that one time with the dog suit (which wasn't even in the manga).
It should be mentioned that Jounouchi/Mai was so liked as a couple that people just assume they were together after the series ended or at least have a mutual crush (especially after the epic Ship Tease and Heroic Sacrificefrom both sides in the Waking the Dragons/Doma arc) until Word of God came out and clarified them as "Just Friends." Right.note idon'tbelieveyou! They weren't called "the only het pairing anyone likes" by fans for no reason despite the large amount of Ho Yay in the series, and the fact that Mai is a frequent target for Die for Our Ship in any Jounouchi-related ship should attest to that. Despite the fact that it would actually be illegal for them to hook up during the timeframe of the series (he's 16, she's 24), they're widely regarded as the closest thing Yu-Gi-Oh! has to a healthy romance.
Puzzleshipping (Yugi/Atem) is probably the most well-known pairing the Yu-Gi-Oh! franchise ever had. In the Japanese version, they even have Affectionate Nickname for the other ("Mou Hitori no Boku/The other me" for Yami/Atem and "Aibou/Partner" for Yugi.) And the two can't seem to stop thinking about the other, and there are just so many subtexts in both the manga and anime, which only makes the fans more excited. Puzzleshipping is pretty much considered canon by most fans.
There are also fans who prefer shipping Judai with Manjoume (the Japanese fandom even refer to them as "Juuman".) But the most amazing case has to be Judai/Yusei, an extremely popular couple. We have the BBT movie to thanks for introducing such a possibility to us - even moreso because for more nostalgic fans, this was the first time many of them had met either character. Even being separated by decades of time couldn't stop the pairing.
Yu-Gi-Oh! 5D's has another unusual case with Jack and Carly, where the pairing was an Official Couple... until they both got Laser-Guided Amnesia, causing Carly to more or less be demoted to a member of Jack's harem (which he decides to dismiss at the end of the series), and causing Jack to ignore her nearly all the time. The number of fics of the two quickly hooking back up is staggering.
Ushio/Mikage is another one. For a brief while, it seemed like Ushio had an unreciprocated crush on Mikage, but this fizzled out when Mikage also became part of the Jack harem. The two of them have become an incredibly popular Beta Couple in Jack/Carly fics.
Yusei is a Launcher of a Thousand Ships, and he ends the story without any canon couple. Do the math. Particularly big offenders include Yusei/Aki, which is probably the closest thing to an Official Couple for him, and Yusei/Jack, for the old-fashioned rival/protagonist pairing. Yusei/Bruno and Yusei/Kiryu are pretty fervent ones, as well, owing to the heavy Ho Yay surrounding their relationships with Yusei.
It's canon that Droite has feelings for Kaito. But the fact that she spends all her time with Gauche, is always in sync with him, and are inseparable have made Droite/Gauche the pairing for both characters.
Yuma/Kotori is also rather unpopular, due to Kotori providing little to the plot and not doing much about her crush on Yuma until the finale. Cat and Anna, however, provided more for the plot and put a lot more effort into getting closer to Yuma. Naturally, they are often the ones paired off with him — Yuma/Anna is the go-to het Yuma ship, largely because of Anna's Ensemble Darkhorse status and the fact that she helped him in the WDC. And this isn't even getting into the slash fandom, who overwhelmingly prefer Yuma/Astral, Yuma/Shark, Yuma/Kaito, or Yuma/III.
Talking of Yuma/Astral, it's essentially the reincarnation of Puzzleshipping, and is similarly often regarded as one Word of Gay away from canonicity. Of the top 25 most-favorited ZEXAL fics on FFN, fourteen are some stripe of Yuma/Astral as of this writing.
And Yu-Gi-Oh! ARC-V does canonically support Yuya/Yuzu. While it is popular, Yuto/Yuzu is moreso; Yuzu spends a significant portion of the first arc chasing after Yuto and trying to figure out his secrets, while he is very protective of her.
The creator really like to troll the shippers here. As of episode 37, Yuto died, probably-but-not-really-merged with Yuya (It Makes Sense in Context) and became his Superpowered Evil Side, which would make the Yuto/Yuzu pairing awkward. Fortunately, Yuya/Yuzu received a lot of Ship Tease on Yuya side in episode 50-51 when Yuya break down when he thought Yuzu was carded by the Fusion Dimension and his feelings were exploited Reiji by telling Yuya to join him to rescue her. As the show continues Yuya and Yuzu get continuous ship tease with each other to the point of being one of the most popular ships in the show.
Eclipsing it in popularity in many circles though, are the variations of "Yucest" (any combination of Yuya, Yuto, Yugo, and Yuri, and possibly Zarc). And for at least a chunk of the fandom, Yuzu's early Ship Tease moments with Masumi were not forgotten easily.
THE couple might just be Zarc/Ray due to the how much ship tease three of the four counterpart ships get in the anime(Yuya/Yuzu, Yugo/Rin and Yuto/Ruri). These three with the Yuri/Serena are all very popular and seeing how these four couples are just different versions of Zarc/Ray, the moment Zarc and Ray was revealed the fanart exploded.
Yu-Gi-Oh! VRAINS: Ryoken x Yusaku seems to be heading this way, producing an astounding amount of fan art in a short time after episodes 43 and 44. If anything else, all the other pairings get far less attention.