On The King of Queens, Deacon was dumped by his wife Kelly (the real life reason being that Kelly's actress accepted a role onAlias), and during this time, the writers very briefly Ship Teased him with Holly. This consisted entirely of one scene, and was never mentioned again, but evidently a lot of fans liked the idea, as Holly/Deacon seems to be a popular pairing in the fandom. However, Deacon and Kelly eventually reconciled (once the actress returned from ABC).
Smallville has a few that don't involve the main character, as the main character Clark was shipped with a half-dozen regular characters (Lana vs. Chloe vs. Lois vs. Lex vs. Alicia vs. Tess) and one fan pairing was never dominant.
Chlollie—the pairing of Chloe with Oliver Queen (aka Green Arrow) was hugely popular, to the point that in the DVD commentary for "Lazarus", producer Holly Henderson makes special note of the fan campaigns in favor of it, particularly when fans sent in thousands of sporks to the SV offices, in reference to a particular Chlollie moment. When they first met, Chloe was clearly wowed by Ollie, and fans immediately jumped aboard the idea of shipping them in fanfic and fanart, especially once they started working together in the Justice League. In Season 9, the showrunners warmed up to the idea, and put them together due to fan demand.
Legends of Tomorrow: From the very beginning, Leonard Snart and Sara Lance (aka Captain Canary) gained a huge amount of shippers. In the first season, there were a few subtle hints at a burgeoning romance, but nothing major (especially compared to the Kendra/Carter/Ray Love Triangle). They do share a brief kiss right before his Heroic Sacrifice, but nothing more.
Fans of 24 were rooting for Jack/Renee almost the moment she showed up. Which led to the fanbase nearly rioting after she was bridge dropped in Season 8.
Veronica Mars and whomever she wasn't with at the time. She's with Duncan? The fans wanted Veronica/Logan. She's with Logan? The fans wanted Duncan back. Not to mention those who wanted her to get together with Weevil or Wallace. Mac and Cassidy were quite popular too, before and after the Season 2 finale.
Eventually the "canon" true pairing of Veronica & Logan took over the show and the fandom, to the point where the crowd funded movie was built around Logan & Veronica getting back together.
Merlin has Merlin/Arthur. The couple was popular from the very first episode and it grew more and more until hundreds of fans began to watch the show for the main reason that Merlin and Arthur looked really good together. On every youtube that the two appear together in, most comments are about the homoerotic subtext in their relationship, about how they are secretly lovers/married, etc. This is sometimes extended to shipping their actors, Colin Morgan and Bradley James. But while no one likes the Offical Couple Arthur/Gwen, people do like Gwen herself, an so Lancelot/Gwen are another fan favourite, often appearing as Ship Mates with Arthur/Merlin.
Nathan Wournos and Audrey Parker of Haven are pretty much the fandom's OTP, despite the fact she practically pushed him into another girl's arms, they don't know much about each other's personal life and at least on one occasion she flirted with a man he despises right in front of him. On the other hand, Nathan's curse of not being able to feel anything seems to be negated by Audrey, which led to a bit of Ship Tease when he kissed her doppelganger to reveal her nature.
In the later seasons, shipping Benson with ADA Barba seems to be more popular than shipping her with her canon love interest Cassidy. Given the near-constant lingering gazes, gentle touches, blatant concern for each other, late-night drinks, and sizzling chemistry — and the fact that actors Raul Esparza and Mariska Hargitay also ship the two characters together — this is not surprising.
'Wizards of Waverly Place'' has Jalex—yes this is an incest fan preferred couple on a Disney show. Justin and Alex act more like a couple than siblings. They were originally intended to be best friends instead of related. Once the post-series movie comes around, the sexual tension is so heavy that casual observers could have mistaken their campfire scene for the start of a romantic kissing scene.
The writers were surprised with the acceptance Puck and Rachel got from the fans, when they first appeared as a one-episode pairing in Season 1 despite the show revolving around her relationship with goody goody Finn Hudson.
The Quinn/Rachel (Faberry) Les Yay pairing could easily make a run for against Puckleberry as the biggest Fan-Preferred Couple on the show.
The pairing won the 2012 E!Online poll for favorite couple. There were so many votes, the site crashed. Also notable is the fact that they defeated Brittana and Klaine, two of the most popular ships on the show, in the final rounds.
The pairing 2012 Zimbio Couples March Madness poll notably beating out Sam/Mercedes (Samcedes), Emma/Will (Wemma) Finchel, Brittana, and Klaine, all of which have been canon at one point or another.
In fact, ship is popular enough to the point that a different phrase containing the word "Faberry" trended each day worldwide for an entire week on Twitter.
Brittany/Santana were definitely way more popular than Brittany/Artie. It was a joke in the fandom for a while about how Brittana fans were getting so fuming-at-the-ears mad over some plotting mass of Bartie fans who didn't actually exist. The eventually became a canon couple.
Payson and Sasha from Make It or Break It have over four times the fanfiction written about them than canon couple, Summer/Sasha
Dawson's Creek: Had Dawson and Joey in the first season, but they were quickly overtaken by Joey/Pacey who retained fandom support for the duration of the show. It's ultimately settled when Joey/Pacey become the official couple in the series finale.
Jeff and Annie from Community evoked this reaction. The various Season 1 DVD commentaries indicate that the pairing was a natural evolution of the characters and actors chemistry and also a reaction to the growing popularity of the pairing among the shippers. In the 2011 E!Online poll they were named the 2011 TV's Top Couple narrowly beating out the more well known TV pair of House and Cuddy from the Fox series "House".
Before they became an official couple in Season 4, The Troy and Britta pairing fit this trope as well mostly as a result of being Ship Mates with Jeff & Annie.
Abed and Annie have a small but vocal fandom. It helps that the character's actors Alison Brie and Danny Pudi are real life best friends and have a good rapport. However, Brie has gone on record as not fully supporting the ship herself.
In Heroes Peter and Claire had a lot of chemistry, leading to a lot of shipping, even after they were revealed to be related. It turned out to just be the actors though, as they are currently were dating.
On Stargate Atlantis the two most popular pairings were John/Elizabeth and John/Rodney. Neither of them were concluded by the writers. The originally intended John/Teyla pairing fell by the wayside as the John, Elizabeth & Rodney triangle shared stronger chemistry and the writers losing interest in relationships changed the intended dynamics. The triangle was sunk after Rodney got together with Jennifer Keller and Elizabeth was captured by replicators. Keller was a heavily disliked character upon her introduction and John became darker and guilt-ridden after Elizabeth's disappearance and never ended up in any official couple, leading the Rodney, John, Elizabeth ships to retain popularity throughout the run of the show.
Keller/Ronon was a lot more popular than the canon Keller/Rodney.
In The Middleman, the Middleman and Wendy, despite the fact that the Wordof God has stated this pairing would never be allowed as long as the original creator remained in control of the show.
Speaking of... Billy. Many viewers found the Dee/Lee pairing came out of the blue, and could never like Dee after what she did to Billy.
Most Better Off Ted viewers ship Ted with Veronica over Designated Love Interest Linda, despite the fact that Veronica is The Stoic who has no interest in a romantic relationship with Ted. It helps that they have already had sex without it getting weird, plus they get along well even though Veronica is Ted's boss and Veronica gets along well with Ted's daughter Rose.
And it's hardly surprising why. Although Kirk did occasionally show genuine affection for a girl (for example, in "The City On The Edge Of Forever"), none of his female love interests were ever brought up again once the episode was over. By the movies the writers just seemed to give up altogether and focus entirely on Kirk's relationship with Spock, and even people who deny that Kirk and Spock ever had a thing have to admit that Spock was by far the closest relationship Kirk ever had, the only person even coming close being his best friend/keeper/mother hen/counsellor Dr McCoy.
Star Trek: Voyager had one in The Doctor and Seven of Nine. The hell of it was that this ship was actually teased at in the show, developed, then out of nowhere was derailed for the universally reviled Chakotay/Seven pairing that capped off the series in its final season. (Speculation is that the producers got so annoyed with Robert Beltran's complaints about his character's lack of character development and sub-par writing that they decided to shut his mouth by slipping Jeri Ryan's tongue in it, which as consolation prizes go is not exactly terrible but which derailed not one but two highly popular Fan Preferred Couples — Doctor/Seven, and Janeway/Chakotay.)
DS9 had a large following for Garak/Bashir. However, once the studio realized that, they forced the writers to phase the Ho Yay out of their relationship and Bashir ended up with Ezri (in the re-launch novels, they break up).
Also, O'Brien/Bashir, which seemed to gain the Ho Yay Garak/Bashir was losing.
Odo/Kira started as this. Rene Auberjonois, almost from the very start, played his character as having deep but unrequited feelings for Kira, which was noticed by the showrunners and given more and more importance in the storyline, and the fans took the ball and ran with it. Though Nana Visitor fought the decision to make them canon in Season 6, fearing it would have negative repercussions for both characters if his feelings were requited, she was ultimately satisfied with how they were handled, and so Odo/Kira has remained a Star Trek fan mainstay ever since.
Trip and T'Pol being teased as an odd mutation of the Official Couple during the 3rd and 4th seasons of Enterprise became a fan favorite. Both times the writers seemed to settle their relationship it was too late in the season and got overshadowed by other plots, and had seen an abrupt ending soon after, the first teased a possible future, the second did as well despite Trip's death. A death which the Star Trek: Enterprise Relaunch novels couldn't retcon away fast enough; the literally did it on the first page.This website is dedicated to fan fiction based on the pairing.
Scrubs: JD/Cox is the most popular ship in the fandom, despite the fact that JD and Elliot end up together and Dr. Cox has been in a stable relationship with his ex-wife since Season 2. It's also kind of ironic because canon-wise, JD and Turk are the ones who have a lot of Ho Yay.
Supergirl: In season one, Kara was shipped with Cat Grant much more often than with her canon love interest, James Olsen. Due to Cat's departure at the beginning of season two, Kara is now most frequently shipped with Lena Luthor, while the show seems to be moving her toward a romance with Mon-El. Mon-El, in turn, is usually shipped with Winn Schott.
Sam/Dean (or "Wincest") used to be the most popular ship in the fandom. Sam/Dean fan shipping has become so popular that it even was acknowledged on the show. The Winchester Brothers' reactions—especially Dean's—to discovering Wincest slash fiction was priceless.
Dean: That's sick.
As of Season 8, "Destiel" (Dean/Castiel) swept in and took the role of the most popular pairing. Just take a look at their section on the Ho Yay page.
While not nearly as vocal as the Ho Yay shippers, the fan-preferred heterosexual couples are Dean/Jo (although it wasn't until Season 5, when she matures and takes a level in badass that the pairing gained more popularity, and any chance of them getting together was effectively squashed when Jo got killed off), while Sam is generally either shipped with his first canon girlfriend, Jessica (often nicknamed "Jess"), despite the fact that she was killed off in the very first episode, or his other Season 1 Love InterestSarah Blake, for being a sweet and normal girl who kept up with the boys pretty well on a case and one of Sam's few love interests that didn't turn out to be a monster (like Madison or Amy) or demon (like Ruby) or despised by the fandom in general.
Jackie and Hyde on That '70s Show. An interesting case, since the writers actually made the two a couple in later seasons... only for them to break up and cause them to slip right back into preferred territory with even more fans then before. Danny Masterson (Hyde's actor) has even tweeted  saying he doesn't understand to this day why they didn't end up together.
In the US version of The Office, nigh everything involving Jim and Pam up until Season 4 had been pretty obviously a shameless, cackling gambit to get this reaction out of the audience.
All the Coupling fans wanted to see Jeff and Jane hook up. They were supposed to in the 4th series, but then Richard Coyle (Jeff) quit the show, and was replaced by the man who would "Mount Jane...I'm not giving you instructions."
The preferred heterosexual pairing is the main character Tori with Andre in a Just Friends romance.
The preferred heterosexual Beta Couple is Cat with Jerkass Woobie Robbie. These two pairings keep the Official Couple Jade and Beck together, form a fleet of Ship Mates, and only leaves Tori's older sister Trina who is more like a guest character than a main character unpaired.
Leverage: There are a lot of Eliot/Parker fics on fanfiction.net, despite Parker/Hardison being the Official Couple now and having had the UST massively pushed from at least Season 2.
Also popular is Eliot/Hardison, for how much they bicker and yet genuinely like one another. For obvious reasons, Parker/Hardison/Eliot is very popular.
The Mentalist had Lisbon/Bosco as a canonical one-sided romance, which, while having the small issue of Bosco being married, also has the much bigger problem of being universally hated because most fans are Jane/Lisbon.
The idea of a Vanessa/Rufus pairing has gained a lot of fans, going so far as many people speculating that she is currently dating Dan only to be close to Rufus. Word of God has sunk the ship but since when has that stopped shippers? For those not in the loop, Dan is not Rufus's brother, as one might guess from that entry; Dan is Rufus's son. Vanessa and Dan are both eighteen or nineteen; Rufus is... well, actually, it's hard to tell, because the timelines are all messed up, but he's the father of a nineteen year old boy, who was conceived in wedlock, so... yeah.
Dan and Blair has also gained quite a strong following that started after heir arc in season 4.
Nate and Jenny were quite popular towards the beginning of the show. They even became canon in Season 2. However Executive Meddling ended it because apparently the fact that Jenny was played by an actual teenager, unlike the rest of the cast, made Chace Crawford uncomfortable.
As of the Season 3 premiere, a lot of people prefer Carter/Serena over any other Serena pairings, including the original alpha couple.
The Guy/Marian ship on Robin Hood ended with one half of it murdering the other. Doesn't stop the shippers.
This one is subject to Vocal Minority, though - most polls of the fanbase at large indicate that they prefer Leonard/Penny. Despite cries of war from the shippers, it also seems the fanbase at large is happy with Sheldon/Amy.
Gilmore Girls ended with Rory single, but Jess/Rory remains the most popular Rory coupling in the fandom.
Barney/Robin: They actually became canon after more than a season of build-up... and then broke up after a few episodes, with Robin getting a new love interest universally hated by the fandom. Although they are soon to be canon again, as they will get married in the future.
Victoria, Ted's Season 1 girlfriend who according to the writers was going to be revealed as the mother if the show wasn't renewed for a second season, was a ridiculously popular love interest, even more popular than Ted/Robin. She and Ted broke up when he (sort of) cheated on her with Robin. She suddenly turned up in an early episode of Season 7 for the first time in six years. The fans were happy, but that rejoicing turned into anger (at the writers, not her) when in the next episode she revealed that she got a new boyfriend almost as soon as she and Ted split up, had been with this new boyfriend ever since, and was now all but engaged to him. Although Ted and Victoria do run off together in the Season 7 finale, it still sinks due to Ted's unresolved feelings with Robin. And with the Finale Season, it seems many fans are accepting Christina Milloti's character as the titular Mother, particularly with sharing the similar quirks as Ted and their interaction together in the future. Nevertheless, the pairing is still fairly popular with many preferring that Ted should have ended up with Victoria over of Robin when The Mother died in the finale, or that it would have been a less bitter pill to swallow had he done so.
How I Met Your Mother must have the by far strangest example of this trope to date. The very premise of the show is built around shipping Ted and Tracy (the mother) and it's what they spend nine seasons building towards. They also spend the last three seasons building Barney and Robin as a couple, focusing the entire last season on their wedding and the second to last episode featuring the wedding itself. Barney and Robin has been a very popular ship ever since Season 1, so a lot of fans were happy that they ended up together. As for Ted and Tracy, most fans were saying that once she actually appears they will probably dislike her because she can't live up to the image Ted has created over the years, but when she eventually did show up she became a fan favorite and people got even more invested in Ted/Mother. In the finale Barney and Robin divorce, Tracy dies and Ted's kids encourage him to go get his ''true'' love - Robin. Needless to say, many fans were shocked andfurious. Unsurprisingly, the alternate finale was much more positively received.
Damon and Elena from The Vampire Diaries have always been a fan-favorite. The producers pretty much switched the endgame to Damon/Elena instead of Stefan/Elena due to the popularity of the relationship and the flash forward in the series finale reveals they stayed together until they died.
Even though after Season 4, Klaus moved to another show and both he and Caroline are getting an incredible amount of Ship Tease with other characters, the majority of the fans still want to see these two together.
Joshua and Lisa on V (2009). Mainly because the two have a nice chemistry and are very protective of one another and - oh yeah! Lisa's canon Love Interest is Tyler.
Super Sentai: Most series feature Ship Tease between the Red and Pink Rangers (or Red and White, if there is no Pink) so in any Sentai where they do not get together, they are likely to be the Fan-Preferred Couple instead. The most prominent example is probably Hikari Sentai Maskman, which has a large fanbase in Indonesia and the Philippines because official dubs of the show were aired there. These fans often state on fansites and blogs that they would have preferred Momoko to be Takeru's love interest, rather than the canon Takeru/Iyal (which later broke up due to Iyal's duties as the new Tube leader). Which is kinda weird since Takeru and Momoko hardly speak to each other or share any screen time.
On the American adaption of Mahou Sentai Magiranger, the fan preferred couples seemed to be Yellow/Pink and Green/Blue. Both were mostly disrailed towards the end of series, but remain popular in fandom.
Back in Japanese fandom, in Tokusou Sentai Dekaranger, while Ban eventually got a girlfriend from The Movie and Umeko gets on with Sen-chan, the spare-pairing between Hoji and Jasmine is slightly a bit more popular than their other options. It helps that Hoji and Jasmine were perceived as the most 'pro' and 'senior' of the team, respectively, and that they had some history; never mind that Hoji nearly embarked on a relationship with another woman (though they were rather tragically torn apart due to Hoji killing her younger brother who was the criminal of the week).
Masumi/Natsuki is universally popular among fans of GoGo Sentai Boukenger, and despite never quite reaching Official Couple status, it gets as much praise and fanworks as the canon Akashi/Sakura.
The ship was later sunk when both actors stated in an interview that the characters had a family-like relationship.
Nanami/Isshu was hugely popular with fans of Ninpuu Sentai Hurricaneger and became an Official Couple on the show, but was sunk by the reunion movie 10 Years Later (released in 2013, ten years after the show's end), in which they have split off-screen and Isshu is now a playboy with many girlfriends. It's done nothing to kill off the ship's fanbase, thus, they're now a Fan-Preferred Couple instead.
Also in Kyoryuger, Nossan/Candelira became incredibly popular with fans after Brave 41 revealed that they had begun to develop feelings for each other (this was also the impetus for Candelira's Heel–Face Turn.) However, they became this trope at the end of the series when the ship was left unresolved.
Kyoryuger seemed to have an unusual abundance of fan-preferred couples; additional pairings that got traction over the season, but were sunk or otherwise unresolved, include Souji/Amy, Daigo/Meeko, and Souji/Rin (the manager of the kendo club at Souji's school), though Souji/Rin was eventually acknowledged as canon in the 100 Years Later feature.
Samurai Sentai Shinkenger had an overwhelming amount of fan support among both Japanese and overseas fans for the pairings of Takeru/Mako, Takeru/Kotoha, and Chiaki/Kotoha (and later in the show, Genta/Kaoru), although nothing came of any of these.
Bobby Goren and Alex Eames of Law & Order: Criminal Intent blur the lines between this and Official Couple. While nothing romantic was implied to have happened between them, it is made explicitly clear that there is nothing they would not do for each other. That line, however, was most likely crossed when Alex quit her job after having to fire Goren, leaving certain "possibilities" wide open.
Many fans of Pushing Daisies wanted to see Ned hook up with Olive. After all, Ned had a Dark and Troubled Past and might have been happier if he had a woman that he actually could touch.
Jake/Heather in Jericho, despite the Word of God's preference for Jake/Emily. (Considering that Jake and Emily were exes at the start of the series, you would think this was the last direction you expected the writers to go.)
On Stargate Universe, the Eli/Chloe shippers seem to be far more numerous than the Chloe/Scott shippers, despite the latter being canon. The single most common complaint about the episode "Light" is that Chloe and Scott's sex scene in that episode came out of nowhere. It doesn't help that Eli is the audience surrogate for the first few episodes, or that Scott had another potential love interest (Lt. James), or that before they had sex, Chloe and Scott had had just one scene with just the two of them, while Eli and Chloe spent much of "Darkness", the episode prior to "Light" together.
Most of them have given up by now, due to a combination of three factors: 1) Eli and Chloe's friendship gets just as much screentime as Scott and Chloe's relationship, 2) Any realistic chance of the ship happening vanished sometime between "Incursion" and "Cloverdale", and 3) the rise of Eli/Ginn caused many Eli/Chloe shippers to jump ship.
Dale Cooper and Audrey Horne in Twin Peaks. Not only fans, but also writers wanted to develop their relationship further in the second season (Mark Frost, the producer, said that it was gonna be the next big thing in the show after the exposure of Laura's murderer). According to Robert Engels, the producer-writer, the script was changed because of Lara Flynn Boyle, who was dating Kyle MacLachlan at the time. Later Kyle MacLachlan tried to justify the decision, that Cooper would not date a high-school girl. However he hooked up with Annie Blackburn, who was only one year older than Audrey (Heather Graham, who portrayed Annie is in fact five years younger than Sherilyn Fenn). Sherilyn Fenn was disappointed with the changes. In 2007 documentary "Secrets from Another Place: Creating Twin Peaks" she stated: "I was not interested in Kyle as a man, but Audrey loved him. I was really into being in those scenes and i thought we had fun chemistry, so... I don't know, I guess chalk it up to unrequited love".
Inspector Thomas Lynley and Sergeant Barbara Havers of The Inspector Lynley Mysteries are shipped far and wide in the (admittedly small) fandom (including by the star of the show himself, who once declared that he'd have liked to see the series end with Lynley and Haversholding hands and walking into the sunset). Although Lynley himself spent much of the series involved with and even married to his university BFF Helen Clyde, when she dies in series 5, all sorts of possibilities are left wide open. Couple that with a not-insignificant amount of subtext - including the fact that Lynley's relationship with Barbara, despite its difficulties, is far healthiernote for a given value of healthier, given how screwed uptheyare than his relationship with Helen ever was, the fact that Lynley will leave Helen behind to go running off with Barbara without a second thought, that they call each other their reason to get up in the morning, and the hug - and there's a good reason Lynley/Havers is, quite simply, the only pairing in the fandom.
Despite a 27-year age difference between the characters, 73 percent of Foyle's War-related fanfics found on Fan Fiction.net as of the beginning of 2012 romantically pair Christopher Foyle and his driver Samantha Stewart. Many fans argue that their relationship on the show is more father/daughter, but Foyle on occasion gently lets the audience know he finds Sam very attractive, and although he initially thinks her somewhat intrusive (and over time is often amused by her youthful exuberance), he quickly begins to admire her ingenuity and allows her to be involved with the solving of cases, treating her for the most part in an egalitarian manner unusual for a man of his generation and time. Add to that a lot of chemistry among the two actors, and fans want RST.
A decade before the term "shipper" was coined, many viewers of the 90s sitcom The Brittas Empire felt that Gordon Brittas would have been better off with his Hyper-Competent Sidekick Laura than his nervous alcholic wife Helen.
Within Doctor Who - as it's 50 years old and all - there's been a few of these. Though early Doctors made no reference to sex or sexuality, since the show's return the fanbase has been more active in supporting relationships between the Doctor and his companions. It began with Rose and Nine/Ten, and continues through to the most recent pairing of Clara and Twelve. Sometimes the series has supported it (though due to The "I Love You" Stigma it maintains, nearly always in subtle ways), while sometimes it has introduced alternate pairings. And on a few occasions, pairings have actually overlapped (for example River/Doctor, with River actually being the Doctor's wife, overlapped both Clara/Eleven and Clara/Twelve). And then there are alternate pairings such as Clara/Danny or cases where the series has intentionally featured a companion who is in love with the Doctor (Martha and Jack are two examples) yet the Doctor has shown no interest in pursuing such a relationship on screen. All this has led to Ship-to-Ship Combat in fandom. But one of the most popular pairings is the Doctor/the Master, with Three, Four, and Five with their respective Masters are most common, and the age of both characters goes a long way to explaining their popularity. The introduction of the female version of the Master, now known as Missy, who openly refers to the Doctor as her boyfriend in one episode and snogs Twelve in another (something not even Clara ever did) has created another fan-preferred pairing, though Ship-to-Ship Combat is also occurring with those who prefer Clara/Missy. Eleven/Amy is also another popular pairing, despite the fact that Amy becomes the Doctor's mother-in-law.
Passions: At one point, many fans of Ethan and Theresa got so disgusted with Ethan's behavior, they began actively clamoring that Theresa be paired with his brother Fox.
Fans also preferred Hank/Gwen.
Kamen Rider Double features Akiko and Terui as the Official Couple. Akiko divides the fanbase between those who like her and those who find her too loud and annoying, and a common opinion expressed on fanboards is that Terui should have got together with guest character Lily, played by fanboy favourite Nao Nagasawa (also known as HurricaneBlue.)
Haruto and Koyomi in Kamen Rider Wizard had a lot of "moments" together, with Haruto explicitly stating that Koyomi is his own "last hope." As of the end of the show, it can't happen because Koyomi is Dead All Along and finally destroyed, leaving the Hope Ring for Haruto and asking that she be left to rest in peace. It still enjoys huge fan following and is even supported by Haruto's actor, who referred to their shopping trip in episode 14 as a "date."
In Kamen Rider Kiva, Yuri Aso first falls in love with Jirou before Otoya wins her heart. Otoya later abandons her for Maya, and most fans want Jirou to have won out, despite the fact he attempted to rape Yuri.
Oh, 30 Rock and the long, convoluted history of Jack/Liz. Tina Fey has been saying No Hugging, No Kissing since the first season, but the ship remains as popular as ever. The show is just so determined not to put them together, giving both a series of love interests which never last. 30 Rock long ago started outright spoofing the idea of Jack/Liz, but this just came off as extra quirky Ship Teases, at least to the shippers. Eventually, they just went out and gave them an Accidental Marriage, although it only lasted one episode. The whole episode was basically just a big Lampshade Hanging, saying that "we know you want Jack and Liz together, but we're not doing it." In the last season, Liz gets married (for real, this time) to someone else. And a few episodes later in "Florida", the final nail in the coffin of Jack/Liz occurs when Jack and Liz discuss why they never had a romantic relationship and agree they were always Better as Friends.
Sherlock/John in BBC's Sherlock, but this is hardly surprising considering it's a modern revival of one of the oldest bromances in literature, and both actors are quite good-looking. The number of fanfics that don't have John/Sherlock as the main couple is really very low compared to those featuring the now canon John/Mary Morstan and the liberally ship-teased Sherlock/Irene or the less-teased-but-more-plausible Sherlock/Molly; and most of those are Mycroft/Lestrade fics that include John/Sherlock as the Beta Couple. Think Merlin/Arthur, only Up to Eleven.
And on the villainous side, Moriarty is nearly always paired with his right-hand man Sebastian Moran from the original Sherlock Holmes story, The Empty House, although Moran barely appears much in the TV series. And keeping with the Foe Yay, there is a fairly decent amount of Sherlock/Moriarty in the mix as well.
On Frasier, Niles/Daphne was always infinitely preferred to Niles/Maris, even though Niles and Maris were married. This preference was largely due to the reason Maris remained The Ghost throughout the show's run: her actions were so horrible and psychotic, and her appearance so bizarrely described that the writers deemed it impossible to ever write dialogue for or cast a character of her level of monstrosity. (Niles and Daphne eventually became the Official Couple). To give you an idea how much the fans preferred this couple, Niles leaving his second wife days after they eloped and Daphne abandoning her fiance at the altar were viewed as positive things because it meant Niles and Daphne were finally getting together.
In the new Hawaii Five-0 fandom, Steve×Danny is the most popular pairing by far.
Despite the fact they constantly date other people, Booth/Bones in the Bones is the fan preferred couple. Which is rather duh and just a matter of "when will they?", but they have thrown in very likable characters as rival couplings.
In Hannah Montana fanfiction Miley is rarely paired with Jake or Jesse, the guys she dated. Instead in canonical fiction (as opposed to falsely categorized stories about Miley Cyrus) she more often paired with Oliver, Lilly, or Mikayla.
Andy and Nancy, from Weeds, although their case is a complicated one. It's been made canon that Andy is in love with her and that she may or may not reciprocate his feelings and they have a tendency to act like a couple regardless of whether or not they're in other relationships at the time, but the two haven't gone past a Fake-Out Make-Out and most fans believe they'll never happen on the show. Still, that doesn't stop them from being countless times more popular than any of their canon relationships.
It did not take long for fans of 2 Broke Girls to latch onto the pairing of Caroline/Max.
Effy/Cook was way more popular than Effy/Freddie ever was, though there was enough of both to lead to Ship-to-Ship Combat.
Mini/Franky aka Minky was easily the most popular ship of the third generation (with the possible exception of Beta Couple Rich/Grace), though, like the example above, it's not so universal that there isn't someShip-to-Ship Combat.... with Mini/Alo. But pretty much nobody liked Franky with her canon love interest, Matty. As a result, there was a huge fan outcry when Word of God said not to expect anything Minky in Series 6.
Fans of the US version seemed to prefer Tea and Tony together.
One of the most popular non-canon pairings within the Firefly fandom is River/Jayne, spurred on by the series' overall theme of Opposites Attract in the three canon romances/relationships and held aloft by more than a little Foe Yay and Belligerent Sexual Tension. The fact that as of the end of Serenity, River and Jayne are the only two characters who are still alive who aren't already paired up ( save Zoe, who is still grieving over Wash) further fuels this reaction.
While Nick is all but engaged to his live-in girlfriend Juliette in Grimm, the fandom loves to pair him off with Monroe instead.
Warehouse 13's fan preferred couple is without question Myka/HG, though there are Pete/Myka shippers as well.
Go to Fanfiction.Net, and you will see that almost every Rizzoli & Isles story is Jane/Maura. It's not hard to see why these two are constantly being shipped, with all the heavy-duty Les Yay and whatnot.
For most of the fifth season of House, fans preferred Thriteen and Kutner to the Official Couple, Thirteen and Foreman. This probably resulted from many fans' interpretations that Thirteen and Kutner were previously being set up as a potential couple, the common sentiment that the Thirteen/Foreman get-together came out of nowhere, and just the fact that Foreman was easily the least popular character at the time. The pairing did eventually gain some popularity, especially once Kutner died.
At the time, there was a circulating theory that the writers' originally intended for Thirteen and Kutner to get together, but when they became aware that Kal Penn was planning on leaving the show, they stopped setting up Thirteen/Kutner and started setting up Thirteen/Foreman instead. This is supported by the fact that Thirteen and Kutner initially had a lot of scenes alone together and abruptly stopped having them shortly before the show started setting up Thirteen and Foreman.
House/Wilson has always been popular, and House/Cuddy was more popular than official couples House/Stacy and Lucas/Cuddy in Seasons 2 and 6, respectively.
Isobel Crawley/Dr Clarkson was this for quite a long time. It was eventually revealed to be one-sided but still proves more popular than the on-and-off ship of Isobel/Lord Merton.
Despite Matthew dying at the end of the 2012 Christmas special, Mary/Matthew remains much more popular than the other possible Mary ships that the writers have tried to introduce.
Atticus Aldridge and Rose MacClare is by far the most well recieved and popular ship involving Rose. Bonus points that it occurred at the time where many consider Rose was Rescued from the Scrappy Heap and that they actually got married.
Joseph Molesley/Phyllis Baxter, given the fact that they are always together, are both Ensemble Darkhorses almost universally loved by the fanbase, and the fact that they are sensible, incredibly kind people, to the point where nobody really ships them with anyone but each other.
Lilly and Scotty from Cold Case, who had a clear Unresolved Sexual Tension in the early seasons (even lampshaded by John Smith, who bluntly asks Scotty, "You get a piece of that? Bet you think about it from time to time.") Lilly and Stillman also have their fans.
While Ally from Austin & Ally has a huge crush on Dallas, fans overwhelmingly prefer her with Austin, even though they're Just Friends. Trish and Dez are rather popular as well.
In Sanctuary, Helen/Druitt is canon; however, Helen/Tesla is more favored both in and out of universe, especially by Tesla.
The Mighty Boosh: Despite the fact that a) Howard and Mrs. Gideon were never a couple, and b) it was obvious that she was never meant to be a serious contender for Howard's affections, it doesn't stop fans from hating her, probably because she distracted from the UST between Howard and Vince. Many breathed a sigh of relief when she did not appear in the other two seasons. The writers themselves, who play the characters, actively encouraged the pairing, and intentionally wrote vast mounts of Ho Yay into their interactions, to the point they even fell in love and kissed in the next to final episode. Noel Fielding and Julian Barratt claimed they were originally going to write in a sex scene, but decided to save that for if they ever decided to make a movie.
Many Three's Company fans over the years have expressed disappointment that Jack and Janet didn't get together in the end.
In The Secret Circle, Cassie and Jake or Faye seem to be more popular than the Official Couple of Cassie/Adam where the show seems to be leading us. Not to mention Faye and Diana to a ridiculous extent based on all the Foe Yay. Wetpaint recently ran a "who should Faye be with" poll. Only Lee and Jake were mentioned in the title and the article itself, but the poll also included Diana. Diana won with over 87% of the vote.
Another Foe Yay pairing, Captain Hook/Emma (Captain Swan), is one of the most popular fan couples to arise from the show. Tumblr alone has a huge Captain Swan fanbase, and more recently, the pair were a nominated for the 2013 People's Choice Awards "Hottest TV Couple" contest, against popular canon couples. As of the Season 3 finale, they're upgraded to Official Couple..
Bridget/Andrew is this for Ringer fans. They technically are a couple, but fans are rooting for them to be a completely honest couple where Andrew knows that Bridget is Bridget.
David/Colby. It seems like half of the NUMB3RS fandom ships these two. The other half ships Charlie/Colby.
The only Official Couple in the entire Red Dwarf series was Lister/Kochanski, yet they are almost universally despised by the fandom - mainly due to Kochanski's role as Replacement Scrappy . The most popular ship in the show is Rimmer and Lister. On Fanfiction.net, they have 243 fanfictions to Lister/Kochanski's 12. Funnily enough, Rimmer was the character Kochanski replaced.
Some fans wanted Phoebe to end up with David the Scientist Guy instead of Mike. The odds were definitely in his favor, what with being Phoebe's First Love, and almost refusing to move to Minsk for his research, showing just how much he loved her. It didn't help that throughout the storyline where Phoebe was torn between the two, David acted like a gentleman towards his rival, while Mike was a complete douche to him in return. Mike comes across even worse when we later find out that he was already in a relationship at the time as well! And he proposed to Phoebe on the other woman's birthday, no less! (He probably didn't know, but still, dick move.)
Many fans (and even the actors themselves!) would have liked to see Joey and Phoebe get together in the end. Sadly the writers thought it would be too cliche (not to mention the fact that they had to free Joey up for the spin-off that Matt LeBlanc signed on for that Lisa Kudrow didn't.)
Chandler/Monica were originally meant to be a quick fling but were so popular with the audience that the writers developed the relationship and eventually married them.
Some LOST fans prefer Jack/Sawyer (also known as Jawyer) to pairing either of them with The Scrappy Kate.
Both Jay/Ebony and Jay/Trudy were more popular than the designated endgame couple Jay/Amber. Most of the The Tribe Fandom seems to actually quite dislike that pairing for various reasons.
There are too many to list in ER, but the most popular are Carter/Abby and Luka/Sam.
Annie and Liam have become this in the Sequel Series to Beverly Hills 90210. It's weird because they experienced Foe Yay in Season 1, became friends in Season 2, started dating in Season 3 with a few breakups in between and broke up in Season 4 and fans want them back together.
The Event has Vicky and Sean. Perhaps helped by the fact that Sean's fiancee is Leila, who gets herself captured at every concievable opportunity and gets more competent characters killed off by being around her! The series itself implies that Vicky is attracted to Sean, so there is some basis for it.
In True Blood, despite the fact that they barely even get to speak between their affair in the first season and their hookup at the end of the third, the pairing of Sam and Tara generates much more squee than either does with their other Love Interests.
Ever since "Escape from the Dragon House", fans have been dying to see Sookie/Eric) happen. Recently though the fanbase seems to be divided on whether Bookie should be reintroduced, or if it's Sooric all the way.
To make matters worse, there's also Alcide who a large section of the fandom (And TVGuide) ships Sookie with.
The pairing of Pam/Tara has progressively become very popular since the beginning of Season 4. Humungous amounts of squee erupted after the Season 5 finale.
Private Practice has Pete and Violet as of now, Cooper and Violet in Season 1, later Cooper and Charlotte until recently.
Addison and Sam, until recently when he started getting indecisive. Addison and Jake, on the grounds he actually likes kids and her.
Also, Naomi and Gabriel.
While Official Couple(s) Ryan and Marissa and (especially) Seth and Summer are very popular in The O.C. fandom, many fans continued to ship Marissa with her short lived bisexual love interest Alex, long after she had dropped off the face of the Earth. It is also never made clear whether or not Taylor and Ryan ended up together, but the fans are nearly unanimous that they did.
Fletcher has a crush on Chyna on A.N.T. Farm, but most fanfiction you'll find will ship him with Olive instead. Oddly enough, they were together in the last 3 episodes of the final season but broke up because Fletcher stays in New York to pursue his dream.
Darren and Nancy are very much this in HollyOaks. Callum and George also have their fans.
The show Faking It seems to be trying to sell Karma/Liam as much as Karma/Amy. Pretty much no one is rooting for the first ship. So far every single fanfic is Karmy and Katie Stevens and Rita Volk seem to ship it themselves. Those that do sometimes pair Liam with Shane.
In the short-lived Ruby And The Rockits, the favorite couple is Ruby and Jordan despite them being cousins. The fact that it's canon from Jordan's side doesn't help.
There was an extreme example when fans almost universally panned Oliver's official relationship with ex-girlfriend Laurel and instead paired him with his partner-in-crime/computer geek Felicity, who started as a one-episode guest character. The writers seem to be aware of Oliver and Felicity's huge popularity and have invested their time to develop their relationship since season 2 (they've been canon since the third).
Oliver/Sara are another popular pairing especially in season 2 when they became something of a Battle Couple together with many hoping that they would stay that way and have the famous Green Arrow/Black Canary following of the comics.
Tommy/Laurel are a very well regarded romance in the Arrow community with many fans regarding them as having far more convincing chemistry and moments together then any of her scenes with Oliver thought season 1. It's pretty noteworthy that the two still have a very strong fan following to this day despite the fact that Tommy's been dead since the end of season 1.
On the Les Yay side of things Nyssa is often shipped with one of the two Lance sisters. On Sara's end the two were together during her time in the league and Nyssa still has feelings for her although the show has yet to clarify if the two got back together again when Sara re-joined the league at the end of season 2. Meanwhile shipping Nyssa and Laurel together has also become quite popular since season 3 due to their shared bonding over Sara's death with them having many cute interactions together and Laurel becoming a major Morality Pet for Nyssa during the next two seasons.
In South of Nowhere fanfiction, Kyla/Carmen is just as possible... or probably more than Kyla/Aiden.
The show 10 Things I Hate About You did plan on having Cameron and Bianca eventually getting together, but was cancelled before they could. Still you will find very little Bianca/Joey fanfiction. The fact that they actually did get together in the original 1999 movie doesn't hurt either.
Evan is engaged to Paige on Royal Pains, but most fanfiction you'll find will pair him up with Divya.
As the series progressed, the character Jeremiah is introduced into Hank Med and almost instantly fell in love with Divya. Unfortunately, due to the relationship she was in at that moment (and Jeremiah's own awkwardness) Divya remained Oblivious to Love. It's even lampshaded in a series premiere commercial Most fans still would've preferred Divya would've ended up with Jeremiah than Raj in the finale.
A lot of people ship Kiera with Kellogg in Continuum due to Foe Yay and Belligerent Sexual Tension; however, it's largely one-way as Kiera is keeping faithful to her husband from 2077. As of season three, Kellogg is dead and Kiera is with a new time-traveling character.
Riley/Danny seems to be this for the Baby Daddy fandom so far. Part of it seems to be that unlike most characters similar to Danny (tall, handsome, super successful), he's actually a really down to earth character who clearly loves and prioritizes his friends and family over the visages of wealth. For reference, the lowest salary of a pro-hockey player is about half a million dollars so Danny doesn't need to live with his brother because of money issues. The back story reveals he liked Riley even when she was "Fat Pants".
Kevin and Macy were very popular in the first season of Jonas due to the both of them being able to accept and understand each others' quirks, not to mention the fact that Kevin was the first of the brothers to tolerate her Loony Fan tendencies. Many fans didn't like it when Macy's personality was changed to make it more compatible with Nick's in the second season.
Crews and Reese are this in Life despite the fact that Reese is dating Tidwell.
The House of Anubis fandom fell for the UST filled Nina and Fabian early on, and shipped them ravenously in the following seasons, even after Nina had left the show. Helps that they also became an Official Couple at the end of Season 1, and then again at the end of Season 2.
At the end of the first season, many fans seemed to like the idea of the pairings being Nina/Fabian, Amber/Alfie, Mara/Mick and Patricia/Jerome, which paired everyone except Joy (who, as a result, would be paired with future character Eddie), and was basically how things ended at the end of that season, anyways. By the second season however, things became much more complicated in the shipping world...
Long before MTV's Faking It even premiered, people were shipping the main characters Karma and Amy together. Being a fictional couple In-Universe helps.
The one constant ship in Agents of S.H.I.E.L.D. fandom is FitzSimmons. However, the SkyeWard shippers are persistent despite the knowledge that Ward being revealed as a HYDRA plant and a villain, and then dying in Season 3 could sink that ship.
From the start of the show, Philinda was a small part of the fandom that grew despite being unplanned by showrunners, despite the fact that they had repeatedly been referred to as Just Friends until Season 4, where they became an Official Couple.
While Fitzsimmons, Philinda and Skyeward tend to be viewed as the 'main' ships, other smaller canon and non canon ships have since been established, such as Skimmons, Fitz/Mack, and Mackelena.
Clarke and Bellamy (a.k.a. Bellarke) from The 100 have always been the show's most popular pairing, even though after two seasons the closest they've come to an onscreen coupling is a kiss on the cheek; it helps that, in the book series, they're an actual couple. However, the Clarke and Lexa (a.k.a. Clexa) ship is just about as popular now (As of 04/06/2017 they have almost equal devotees on Archive of our Own, with Bellarke winning out by a tiny margin- like, 10 out of 8000+ tiny)
A side note on this one, due to the spilling over of the 100 fandom into the Fear the Walking Dead fandom, the most popular ship in that fandom at time of writing is between Alicia Clark and Elyza Lex- who, for the information of non-fans, is a fan made character to allow for this ship in the aftermath of Lexa's death in the 100 (Elyza Lex is a play on the character's names with the actresses- Lexa is Alycia Debnam Carey, while Clarke Griffin is Eliza Taylor, therefore Alicia Clark is Alycia Debnam Carey and Elyza Lex is Eliza Taylor)
Matt/Claire in Daredevil, due to Karen Page being a Base-Breaking Character and a strong chemistry between the actors despite being sunk by Matt himself. Some fans even said they won't mind if the ship is the show's main couple over some of Matt's more popular girlfriends from comic book such as Elektra, or ship them anyway despite knowing that it won't last. Of course, by Luke Cage, Claire more or less settles for Luke.
Karen Page / Frank Castle ships started popping up almost immediately after Season 2 dropped, quickly becoming the most popular Karen pairing. A major reason for this is their complete unfiltered honesty with one another, which was a breath of fresh air in a show full of people keeping secrets from one another (and especially from Karen). This despite the fact that the ship itself has a few complications of its own.
The The Astronaut Wives Club fandom seems to have really latched on to the pairing of Max and Louise, particularly given Alan's characterization early in the series.
Jax and Emma in Every Witch Way, to the point where fandom literally voted in their preference to make them the show's official couple.
Many fans of Sesame Streetlike the idea of Elmo and Zoe together. There's no romance in canon due to their young ages, however the series pushes Elmo and Abby as friends more than Elmo and Zoe. Most of the fans likely outgrew Sesame Street before Abby appeared or early into her run.
Riverdale: So far the most popular ships have been ones that, ironically, do not include Archie or his eternal Betty and Veronica dilemma. Betty/Veronica are shipped togethermore than either seems to be shipped with Archie. Betty/Jughead is also massively more popular than the traditional Archie/Betty. Betty/Jughead's popularity has only gained popularity since becoming official. Many are hoping that the show abandons the classic Betty/Archie/Veronica love triangle all together to instead focus on building other relationships.