On The King of Queens, Deacon was dumped by his wife Kelly (the real life reason being that Kelly's actress accepted a role on Alias), 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. It can't really be argued which Clark pairing was the most dominant overall, as the base was highly fractured over the issue of who to pair Clark with (Lana vs. Chloe vs. Lois vs. Lex vs. Alicia, and even some Clark/Tess supporters). At best, it can be argued which ships may have dominant at different times in the show's history: In the very earliest handful of episodes, Clana may have started out with a majority of support back when it was seen as "cute," but as Lana became increasingly unpopular, Chlark (Clark and Chloe) overtook it, and may have been the main fan-preferred ship before Lois's arrival, as Chloe was seen as a foil against the widely-reviled Lana (many fans freely admitted that they were only shipping Chlark as an alternative to the now-unpopular Clana, until Clark met his destined future with Lois, knowing full well that both Clana and Chlark were equally Doomed by Canon). Then once Lois arrived, many fans rallied around her, welcoming her as a harbinger of Clark's destined future as Superman and enjoying her witty lines and Erica Durance's acting (though many ardent Chloe-supporters still stayed with the Chlark ship) It can be argued that Clois had become the majority pairing by the end, partially helped by Lois's continued character development and increasing importance in the story, as well as the fact that Chloe got involved in another hugely popular pairing: Chlollie.
Chlollie—the pairing of Chloe with Oliver Queen (aka Green Arrow) was hugely popular (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. At first, they are just Friends with Benefits, but the relationship evolves into a full-blown romantic relationship, while the witty banter and chemistry between Allison Mack and Justin Hartley arguably helped increase the pairing's popularity more and more, till the point where in the Grand Finale the writers, despite DC Comics's pairing of Ollie with Black Canary, couldn't bring themselves to break Chlollie up, and left a vague ending where Chlollie may or may not still be together seven years later...but implying that, either way, there is now a child who is probably theirs.
Lana was rather unpopular, as was the Clana ship, so the pairing of Lexana (Lex Luthor and Lana Lang) did seem more popular than her with Clark as it managed to imbue Lana with some measure of depth while keeping her as far away from Clark as possible (by S6, almost all fans viewed Clana as a toxic relationship). When Lex and Lana were married, some who previously hated Lana even began to like her as they thought (since Clark and Lana was Doomed by Canon) that Lana may be corrupted by Lex, which would have finally given her a measure of coolness as a Dark Action Girl and Femme Fatale. Eventually this was not the case, sadly. Lana left Lex for Clark (who she didn't end up with either) and Lexana was finished—along with the fandom's patience with her.
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.
Merlin/Arthur. No, really. 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. Not to mention there's another fanbase, almost as big as the Arthur/Merlin one, that is completely dedicated to shipping their actors, Colin Morgan and Bradley James.
Despite the writers appearing to legitimately foster almost any pairing they can, just to keep the Merlin fandom harmonious, there are still certain factions of contention between the arguably duller canon pairing of Arthur/Gwen and the buckets of Ho Yay between Arthur and Merlin. A quick check on fanfiction.net will show you that there are roughly five times as many Merlin/Arthur stories than Arthur/Gwen ones. Although in fairness, you can't really blame the fans for this one. Since the show began, the writers have invested a great deal of time and effort into the development of Arthur and Merlin's relationship, and a minimal amount into Arthur and Gwen's, to the point where the latter feels like a Satellite Love Interest by comparison.
Lancelot/Gwen are another fan favourite, often appearing as Ship Mates with Arthur/Merlin.
Merlin/Morgana are quite popular too.
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.
Just watch the last Wizards of Waverly Place movie and you will see that even the producers have become Jalex fans (along with almost every fan of the show). Seriously, Justin and Alex act more like a couple than siblings. This is either due to the creators' inability to portray a "clean" brother-sister relationship or they just did it on purpose. Perhaps they realized that they made a great mistake when they made Justin and Alex brother and sister instead of best friends as originally intended.
Fans also like to pair Harper with Max even though she has a canon boyfriend in Zeke.
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. And even though the show is completely driven by her relationship with goody goody Finn Hudson, the "Puckleberry" fanbase is still strong after two seasons. But the Quinn/Rachel (Faberry) pairing could easily make a run for Puckleberry's money as most popular Fan-Preferred Couple. Really though, it's hard to pick just one in the huge anddivisive Glee fanbase.
Before they became canon, 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 pairing of Rachel Berry and Quinn Fabray (Faberry) 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.
They also won the 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.
It's also worth noting that Faberry also has more fanfiction (over 8000) than the canon Finchel (over 5000).
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 One DVD commentaries indicate that the pairing was a natural evolution of the characters and actors chemistry and also a reaction 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 House and Cuddy.
Before they became an official couple in Season Four, The Troy and Britta pairing fit this trope as well.
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.
Nowadays, the most popular pairings seem to be Peter/Sylar, Sylar/Claire, and Claire/Elle none of which were ever canon. There's also a small fandom for Mohinder/Matt after the two of them acted as Molly's completely straight fathers.
On Stargate Atlantis the two most popular pairings were John/Elizabeth and John/Rodney. Neither of them were concluded by the writers.
Originally the writers had plans for John/Teyla, but the stronger chemistry John had with Elizabeth and Rodney (and unclear shipping agenda) changed the relationship dynamics. Eventually Rodney hooked up with Keller causing a Ship Sinking and Elizabeth was captured by replicators.
Even then, fans latched onto the fact that it was after Elizabeth's disappearance that John's character became much darker and guilt-ridden and that he was the only main character to remain single at the end of the series. This led to even more intense John/Elizabeth shipping.
Keller/Ronon is generally preferred over Keller/Rodney.
Teyla/Anyone got a pretty strong fanbase after Teyla got paired off-screenwith a character who'd never even been mentioned before. And who showed absolutely no chemistry with her (or acting ability for that matter) when he finally made an on-screen appearance. Made even worse when the writers passed on numerous opportunities to kill of the character; while nobody cared enough for him to get Scrappy-level hatred, nobody liked him either.
Kanaan's very existence was an example of Real Life Writes the Plot. When Teyla's actress became pregnant, it had to be acknowledged onscreen, and then something had to become of the baby. So Teyla's one true love becomes... someone who exists just enough for us to know who's babysitting once Teyla returns to action. The writers felt that retroactively pairing Teyla off with one of her fellow main characters would've been weak, because fans would've wanted to know how they got together.
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 six, 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. 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.
Supernatural: Sam/Dean or Wincest used to be the most popular ship in Supernatural 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) seems to be the most popular pairing. Though it received a similar (if less vitriolic) fate in being shot down by a CW executive.
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.
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.
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 in the Gossip Girl fandom (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/Blair has also gained quite a strong following.
Dan/Blair is more accurately a subversion of the trope. While they certainly have a loud and passionate fanbase it turns out that for the majority of the viewers they are the fan detested couple. When they did get together in season five they trended world wide on Twitter because of the adverse reaction the general viewing audience had and the episodes when they were together had the lowest ratings in CW network history. Those who ship them remain passionate about them but it's more than obvious at this point that the writers mistook "loud minority" for "fan preferred".
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 of How I Met Your Mother. 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.
Damon/Elena from The Vampire Diaries. However, the producers of the series have repeatedly said that Stefan/Elena are the true love story of the show and always will be, implying that Damon/Elena do not have much of a chance to be a couple or endgame, much to the Damon/Elena fans dismay.
Stefan/Elena in season one before they became an Official Couple within the same season. Most viewers of the show were rooting for the central love story of the series, especially in the first season. Although Stefan/Elena still have a large, solid fan base, the vocal and large support for Stefan/Elena has appeared to have died down since they became a canon couple.
Despite her canon relationship with Matt, whom she admits to love, Caroline is mostly shipped with Tyler and Stefan. And the fans who don't like Damon with Elena seem to like him admitting feelings for his onetime girlfriend/food supply.
Now that Tyler/Caroline has become an official couple fanfic writers have shipped Caroline with Big Bad Klaus whenever they're not shipping her with Stefan.
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 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 they were both probably the most 'pro' and 'senior' of the team, and they share a past together. Never mind that Hoji nearly got on a relationship with another female (although they kinda broke up tragically)
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 if not more than the canon Akashi/Sakura. (The ship was later sunk by Masumi's actor, who stated that the characters had more of a father-daughter 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.
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 were seen as mostly asexual, Rose and Nine or especially Ten is prevalent amongst the fans on fanfiction.net. However, Doctor/Rose is blitzed by, of all things Doctor/Master which turns up over seven hundred thousand google results, over Rose/Doctor's one hundred thousand. Three, Four, Five and Ten with their respective Masters are most common, and the age of both characters goes a long way to explaining their popularity.
Amy/Eleven was also briefly but extremely popular in the Eleventh Doctor's first season, despite the fact she's now married to Rory.
There is also Doctor/Romana II, they were obviously close and the fact the actors later married is a fact in their favour. Also in their favor is the fact that they're the same species, so the usual objections to a Time Lord Interspecies Romance didn't apply to them.
Word of God suggests that the actors got so wrapped up in their characters that they got married mostly because their characters were in love. The marriage was not particularly happy or long-lived.
Doctor/Clara, dubbed 'Whouffle', exploded into popularity after The Snowmen aired, and became even more popular as the second half of Season 7 progressed. The fact that Matt Smith and Jenna Louise Coleman's chemistry was amazingly good didn't help matters.
Steven Moffat seems to like teasing the pairing in interviews, even going as far as sying the Doctor was 'smitten'.
Doctor/Clara fans had their hearts broken by Matt Smith's decision to leave after only spending half a series with Clara and then getting replaced by the MUCH older Peter Capaldi.
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.)
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 likely-soon-to-be-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, despite the fact that we don't even know if Moran exists in this universe.
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 that the almost-universally despised season finale has Danny get back together with his ex-wife, Rachael.
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 - at least, those who weren't offended by the Unfortunate Implications of having a "confident lesbian" character sleeping with a boy. But even fans who wanted Tea with a girl had trouble rooting for her with one-dimensional canon girlfriend Betty, and tended to ship her with her friends Michelle and Daisy instead.
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.
The Borgias has Cesare/Lucrezia in a similar vein to Justin/Alex above. Although there's probably nothing accidental about it - the historical Borgia siblings were rumored to be lovers.
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.
There is 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 abruptly stopped having scenes together right around the time Thirteen and Foreman were starting to be set up.
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.
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.
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 of the The Mighty Boosh 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.
Many Three's Company fans over the years have expressed disappointment that Jack and Janet didn't get together in the end.
Ben and Felicity, apparently, even if he was a slimy git.
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.
A minority of Once Upon a Time fans like Snow and Charming but dislike Mary Margaret and David. Weird as they're the same people trapped in different realities/personas. Part of it may be since in the human world, David is married, and the affair that results from it turns out rather ugly.
And judging by the response of "Skin Deep", Rumpelstiltskin and Belle. Much like on LOST, side couplings end up more compelling than the show's primary romance. Lesson: OTP can't be forced. Rumpelstiltskin and Belle (commonly known as "Rumbelle") narrowly missed winning the most popular TV couple award for 2013. This was against popular fan couples as well as canon couples, such as the one they lost to: Dean/Castiel from Supernatural.
Crack Ship/Foe Yay pairing of Regina and Emma aka "Swan Queen" is a popular fan couple. They are in fact second only to "Rumbelle" in popularity. Both actresses are aware of it, and Lana Parrilla (who plays Regina) at least has said while that was not her original intent, she will fully support it if the show made the couple canon. Make of that what you will.
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 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.
Friends: Many fans wanted Phoebe to end up with David the Scientist Guy instead of Mike. 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!
Some 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.)
Also Chandler/Monica who 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 Sawyer/Juliet just because they're so damn sick of the Jack/Kate/Sawyer love triangle.
Most of the fandom, given the question, will probably tell you that their favorite couple on the series is Desmond/Penny, Jin/Sun, or Rose/Bernard.
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.
Although there are a large amount of Carly/Freddie shippers, Sam/Freddie is still by far the most popular ship amongst fandom. This is despite Freddie harbouring a strong crush on Carly for most of the seasons. It doesn't help that producer Dan Schneider is rampant with the constant Ship Tease, even throwing in a four episode arc dedicated to Sam/Freddie (which, although played as a Deconstruction of their relationship, ended with them saying "I love you" to each other and making out in an elevator). However, all the actors have said to prefer, and it's been strongly hinted, that the series will most probably end with the protagonists remaining as platonic friends.
Big Time Rush has Kendall/Logan, and James/Carlos to a slightly lesser extent.
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.
Not really that remarkable. About three episodes after Ben was introduced, it was already completely obvious that he was being set up as a love interest for Leslie. The fact that the shippers went for it before it became canon just means that the writers did their jobs well.
Before it was Ben and Leslie, it was Andy and April. Naturally, the shippers lost interest in Andy and April after they actually got together. Fortunately, that was about the time when Ben was added to the cast, so they had a new romance to get excited about as the old one concluded.
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) and 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.
Darren and Nancy are very much this in Holly Oaks. Callum and George also have their fans.
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.
In Arrow, Tommy/Thea is becoming quite popular to the point where the announcement Roy would be introduced as a love interest for Thea drew ire.
Even more popular is Oliver/Felicity, despite Laurel's status as Official Love Interest.
Tommy/Laurel is popular, despite Ollie and Laurel seemingly being destined to become the Official Couple (which, with Tommy's death, now seems inevitable), since they actually have something resembling chemistry.
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.
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. Not to mention that 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.
After "Necromancer" a lot of fans have started shipping Jenny and Irving.
Danny and Lacey in Twisted was this before the show even started airing.
Tess/Karen is quickly starting to become this as well.
Despite both having a string of various love interests of various genders and species, Howard and Vince from The Mighty Boosh are so popular it's virtually impossible to find fanfictions about anything but howince. 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 Mighty Boosh movie. Now that rumours of a fourth season or a movie are popping up, fangirls are going wild.
Rayna and Deacon on Nashville became this more or less from the pilot, helped by their emotional history (e.g. his being the father of her firstborn). And if Juliette decides to become more than friends with Avery, most of the viewers wouldn't complain about that either.