In the Miss Marple book 4.50 from Paddington, Lucy Eylesbarrow had two suitors, Cedric Crackenthorpe and Bryan Eastley. In her "Secret Notebooks", Christie reveals that Lucy would end up with the former, even though many fans find him the more unlikable of the two options. The one that most readers really want Lucy to marry is actually Inspector Dermot Craddock, whom she interacted with once or twice. At least one adaptation run with this, making Inspector Craddock (or, at least, his stand in) Promoted to Love Interest.
In The Sittaford Mystery, the intelligent heroine Emily Trefusis turns down a proposal from journalist Charles Enderby in order to be with James, the "project" fiance, because she says he "needs" her more than Charles does. Many viewers see Charles as a far better match for her, intellectually and otherwise.
One of the oldest examples of this is shown in the Portuguese/Spanish (its authorship is disputed) medieval romance Amadis Of Gaul. Except that in this case it's not so much Fan-Preferred Couple as King Preferred Couple. To further elaborate: the hero Amadis is inextricably faithful to the princess Oriana. During one of his quests, however, one lady Briolanja falls desperately in love with him, and puts him in jail because he refuses to go to bed with her. Apparently the king of Portugal at the time, D. Afonso, really liked Briolanja and wanted her to have a happy ending, so he himself ordered the book to be changed, and have Amadis get hitched with Briolanja (with Oriana's permission, otherwise he'd die... it's a long story). This is retconned in later editions of the book, where the "author"/compiler himself narrates this version of the story, but immediately says afterwards something along the lines of "but this is just the king's whim and not what really happened". And then goes on with the "original" version. It's bizarre.
The Bad Guys: In the books, Mr. Wolf has a crush on Agent Fox and the two develop mutual attraction as the series progresses, but a lot of fans prefer the chemistry between Mr. Wolf and Mr. Snake, especially because of a part in Book 5 depicting a jealous Snake thinking Mr. Wolf likes Agent Fox more than him. This continued into the film due to Mr. Snake's Platonic Declaration of Love and their climactic hug. While a lot of fans feel that the film versions of Mr. Wolf and Diane (an expy of Agent Fox) have better chemistry than their book counterparts, Wolf/Snake remains the most popular ship in the fandom.
Carrie: There is not a lot of shipping in the fandom for the book or its three film adaptations, but what little there is seems to be focused on Carrie/Sue rather than Sue/Tommy. This is mainly due to Sue being The Atoner for her part in bullying Carrie, to the point of turning in herself and her friends, as well as having Tommy take Carrie to the Prom. This only increased following the release of the 2002 and 2013 film adaptations, which both up the Les Yay aspect between the two. As well as the former seeing Sue reviving Carrie and the two heading to Florida together after the prom massacre.
Carry On provides us with an odd Zigzagged example. Carry On is a companion book to Fangirl, and the story it tells is framed as Slash Fic of the (non-existent) Simon Snow series. The Official Couple of Carry On is Simon/Baz, but in Fangirl they're framed as the Fan-Preferred Couple of the Simon Snow series, where Simon was paired with Agatha. The real-world fandom absolutely adores Simon/Baz, and doesn't ship either of them with anyone else. It seems that framing your Official Couple as a Fan-Preferred Couple really gets the fans on board the ship.
Casteel Series: A lot of readers preferred Heaven to be with Troy instead of Logan, even after Troy was revealed to be Heaven's uncle. This is because, aside from incest not exactly being rare in Andrews' works, Troy was the Troubled, but Cute guy female readers swooned over who actually turned out to be more thoughtful and caring towards Heaven than Logan was, making readers wish that he didn't have to be related to Heaven.
Edmond Dantes/Mercedes Herrera in The Count of Monte Cristo. They actually were canon for a while (in fact the reason the plot kicks off is that Edmond is about to marry her, prompting his resentful "friend" Fernand to participate in the plot against him), but events occurred to split them apart. Many fans do prefer Edmond/Mercedes to Edmond/Haydee, including the makers of the 2002 film, most likely due to the Values Dissonance that comes from the Count's adopted daughter falling in love with him and getting it into his head that she doesn't want fatherly love from him.
In Darkest Powers, Derek and Chloe were the fan preferred couple from the very first book, despite Derek's brother flirting with Chloe and Chloe tentatively reciprocating.
By the end of the light novel continuity of The Devil is a Part-Timer!, the titular demon lord Maou Sadao ends up with Chiho Sasaki. However, at least a good chunk of fans prefer Maou to end up with Emi Yusa, the Hero, due to their enemies-to-lovers dynamic, said dynamic fitting in with their respective character arcs of Maou becoming a better person and Emi learning to see the good in him, the massive amounts of Ship Tease, a perception that they have better chemistry, and basically adopting and raising a child together. Chiho, meanwhile, is widely considered an annoying Creator's Pet who gets undue amount of Character Shilling, a mere naive schoolgirl who does not share that same connection with Maou, and a static Satellite Love Interest who's character begins and ends with "crushing on Maou", result in her "love" coming off as shallow infatuation and the pairing being considered forced and boring (and creepy considering she's a teen and he's an adult). Needless to say, the light novel ending drew a lot of backlash from said fans.
While the Discworld series consists of 41 novels, with countless official couples populating them, one fan-preferred pairing of note would be Sam Vimes/Havelock Vetinari. Although Sam Vimes is married to Sibyl in the novels and Vimes/Sibyl has fans and is respected in its own right, Vimes/Vetinari has had the biggest presence since much earlier days of fandom, likely in part due to Sam Vimes being more-or-less the main character of the City Watch novels, and Vetinari being a very major player in those same novels, not only interacting with Vimes frequently but seeming to gain most of his current Manipulative Bastard-playing-the-most-effective-Xanatos Speed Chess personality with every appearance - and often interaction with Vimes - in them.
Fitz/Eight is so popular in the Doctor WhoEighth Doctor Adventures, even the authors ship it! Both of them are canonically bisexual, and the Doctor has No Sense of Personal Space and has kissed Fitz more than once just because he was happy to see him. Fitz has on a few occasions admitted to having a crush on the Doctor, and eventually flat out admits he's in love with him. While the BBC didn't really allow anyone to explicitly portray the Doctor as in love with another man, many of the writers slipped in hints whenever possible, and towards the end of the series's run, most of the recurring writers had given up trying to evade the censors because it was obvious the censors themselves didn't care.
In The Dresden Files the majority of the fanbase shipped Harry/Murphy (who are best friends on the edge of Relationship Upgrade) over the official Harry/Luccio. It turns out that Luccio was brainwashed into dating Harry, and they break up. And since Changes there's been more official Ship Tease for Harry/Murphy.
Weirdly, the fanbase has a large slice of Yaoi Fangirls (Fanboys?) who ship Harry, the Big Good, with Marcone, the Affably Evil mob boss. This is strange because Harry's narration has a lot of Male Gaze, and he is Ambiguously Bi at most. At any rate, this one isn't about to become canon.
Many — possibly even a majority — of fans of the Earth's Children series wished Ayla had stayed with charismatic Ranec from The Mammoth Hunters. Indeed it seemed like Ayla only chose to go back to Jondolar (who was being a petulant ass throughout the book) because Ranec is black. That... or Ayla's a size queen.
There's also those who think Baby ate the wrong brother ship Ayla/Thonolan, Jondolar's brother, who was dead before Ayla and Jondolar ever met.
A good chunk of the Emily of New Moon fandom favours Emily/Dean over Emily/Teddy, as even fans of Emily/Teddy find him a painfully dull, flat character with all the personality of a paperclip.
In Georgina Kincaid, Georgina/Seth is often ditched in favor of Georgina/Carter, Georgina/Jerome, and Georgina/Roman.
The Great Gatsby: Nick/Gatsby, nicknamed "Natsby" by the fandom, is widely preferred over Daisy/Gatsby, Jordan/Nick, or just about any other possible pairing in the book, mainly due to the vast amounts of Ho Yay to back it up and the fact that it's the only pairing that could conceivably be, you know, functioning and healthy. This continued into the film adaptations, most notably the 2013 film. The pairing also easily dominates fanfiction for the book and has a strong following on sites like Tumblr.
The Grisha Trilogy has a rare case of two involving the same person. Alina/The Darkling and Alina/Nikolai are both more popular than Alina/Mal. This seems to stem from a large number of fans finding Mal, Alina's main love interest, boring at best and borderline abusive at worst. A good number also feel Alina simply has more chemistry with the others.
Draco/Harry fanworks completely outnumber all other pairings on Archive of Our Own. As of December 2020, Draco/Harry fanfiction has over 43,000 stories, compared to the next popular pairing on the same site (Sirius/Remus), with just under half that. Canon pairings Ron/Hermione and Harry/Ginny place third and seventh, at around 13,000 and 10,000, respectively.
Draco/Hermione is the most popular pairing involving Hermione within the fandom and the second most popular involving Draco (after him with Harry). Despite the canon Hermione/Ron still being very popular in the fandom as well and Draco/Hermione being controversial within the fandom, Draco/Hermione outranks Hermione/Ron on almost every site. This is often attributed to Hermione's actress in the films, Emma Watson, admitting several times that she had a crush on Draco's actor, Tom Felton, and fangirls wanting to live through Hermione being with the Trope Namer for Draco in Leather Pants.
Neville/Luna is very popular, in large part due to Pair the Spares. Neville and Luna don't have any canon pairings listed in the main story, Neville's partner listed in interviews has almost no interaction with him, and Luna's partner is only revealed in interviews with the author as Rolf Scamander, meaning that pretty much any pairing for them is a Fan-Preferred Couple by default, and it has the benefit of leaving all the main students wrapped up. This has led to the fandom term "Rolfing", a derisory phrase applied to pairings that only occured through Word of God stating a canon character got together with a character that never appeared in the text proper. It does not help that in the movies, they actually do have romantic feelings for each other (although according to Word of God, their relationship would only have been a "summer fling" or something along those lines before they go back to being friends). Ginny/Luna outclasses it in some circles, including on AO3, but hasn't quite caught on in the broader fandom.
Lupin/Sirius vastly overshadows the canon Lupin/Tonks pairing. It is so popular, that many fans actually thought the two characters were canonically together, including the two actors. Back when the series was still running, even sites like Sugarquill that only accepted "canon pairings" (meaning either very heavily hinted-at ones or ones that were canonically together) would often allow Lupin/Sirius, as they were so certain it was a thing. Even when it was rendered impossible, the utter lack of romantic development between Lupin and Tonks certainly didn't win a lot of followers.
At the height of the fandom's ship wars during the three-year summer and for some time after, this title would go to Harry/Hermione, which rapidly ascended into legend for being perhaps the largest and most aggressive faction in Ship-to-Ship Combat history. This mostly owed to their status as the male and female lead, their generally more amiable interactions as opposed to Ron/Hermione's Belligerent Sexual Tension, and the film adaptations teasing it (especially since their actors did have a sweet chemistry going on). On this wiki it was a major factor in Ron the Death Eater being named. Even mainstream publications were known to remark on it. That said, after it canonically sunk, it tumbled quite a bit in the rankings, currently placing tenth on AO3 and being a very common target of mockery due to its aggressive following and rather "vanilla" setup, but nevertheless retains a dedicated fanbase who still widely prefer it over the canon pairings. Suffice it to say, the fans felt pretty vindicated by the 2014 Wonderland magazine interview between Emma Watson and J. K. Rowling where Rowling admitted that there was an element of Wish-Fulfillment behind her pairing Hermione and Ron togethernote She's never said it in so many words, but as it's known that Hermione was based on Rowling herself at a younger age, and Ron on a very close friend of hers from her adolescent years, it's pretty easy to connect the dots and that Harry and Hermione were (in her own words) "in some ways, a better fit."
The Hollows: Despite the fact that Rachel and Trent end up together at the end of the series, most fans ship Rachel with her roommate and best friend, the bisexual vampire Ivy. This is mainly due to these fans feeling that the two have better chemistry and the series having multiple people mistake them for lovers. Most fanfiction for the series is Rachel/Ivy, with it having a little over six times as many fics about it as Rachel/Trent on AO3. It is also easily more popular than Ivy's canon ship with Nina.
Helen/Hector. Helen is/was the queen of Sparta and subtly derides Paris for letting Hector do all the fighting. Hector is a noble warrior who treats her courteously, even though he has every right not to. Since Helen openly wishes that Paris was more like Hector and Andromache is rather flat as a character, you can see where people are coming from.
And of course, on the other side of the war, there's always Achilles/Patroclus. They have been speculated to be lovers ever since ancient time, including by Plato.
Many readers have expressed a preference for Wilfred/Rebecca over Wilfred/Rowena. This was intentional. Rebecca is clearly the heroine of the book (more so than Ivanhoe as the hero); the reason they didn't end up together was that the canon couple had been in love for a long time and Rebecca would never marry a Christian. This one is a rare case of the author himself being one of those who prefers the couple — he flat-out says so in the introduction!! He didn't have it happen though, as he explained, because it would have been an over-cheap and unrealistic morality lesson to have characters rewarded in this life for their good deeds with a successful spur-of-the-moment romance.
And then there are the readers who are okay with Wilfred/Rowena… because they ship Rebecca with Sir Brian instead, though a) he kidnaps and attempts to rape her b) she adamantly refuses him many times and he still doesn’t take the hint c) even without all that, they are of different religions as well and, in addition to this, he is a Templar (except in some adaptations) and can't marry.
You'll be hard-pressed to find any fan of the Land of Oz series who didn't ship Dorothy/Ozma at one point. The two get along well, have a lot of sweet interactions, and outside of the classic characters from the first book, Dorothy's known her the longest. They even kissed a few times. Some authors have tried to avert the romantic implications by giving them male love interests, but it never stuck.
A pre-television example due to it being autobiographical: Jo and Laurie become best friends and understand each other better than anyone else, but when the Relationship Upgrade moment comes, Jo uses the old "Like Brother and Sister" excuse, and at some point, she wants Laurie to marry her little sister Beth. The two end up marrying different people (Jo marries her Big Brother Mentor Fritz, Laurie marries Jo's other sister Amy since Beth dies)... and continue to remain best friends and confidants.
Meanwhile in the continuing sagas of Little Men and especially the latter Jo's Boys where the cast is all grown up — some fans still prefer Nan/Tommy over Tommy/Dora even though the former ship was sunk over and over by the author. Dan dying in the epilogue of Jo's Boys outraged everyone, especially when some wanted to see Dan/Bess happen. Other fans also liked the thought of Dan/Nat or Dan/Nan.
The Lord of the Rings: Many readers were taken by surprise by Sam's sudden interest in otherwise barely mentioned Rosie, after a lengthy novel of obsessive devotion to "Master" Frodo. Compare the amount of Rose/Sam fanworks to Frodo/Sam.
Quite a few Janeites wish Mansfield Park had ended with Fanny/Henry Crawford and Edmund/Mary Crawford instead of Fanny/Edmund, despite the fact that Austen always strives to show that true love arises from similarity of character and that bad boys will not change for a good girl.
The Maze Runner: While Thomas is paired with Brenda in canon, most fans ship Thomas and Newt (Newtmas), mainly due to the Ho Yay between them and Newt being a fan favorite. This carried over to the films where the chemistry between Dylan O'Brien and Thomas Brodie-Sangster is seen as one of the highlights. Thomas/Newt has over 3000 fics on AO3, while Thomas/Brenda only has 105. Those who don't ship them usually pair Thomas with either Teresa (Thomesa) or Minho (Thominho).
Les Misérables: A large number of fans think that Marius chose wrong in picking sheltered ingenue Cosette over street-smart Stalker with a Crush Éponine. Never mind that he didn't know the latter loved him until right before she dies in the book, and never in the stage show.
The Moomins: While Moomintroll and Snorkmaiden, who get the most canon support for their relationship, are by no means an unpopular pairing, it is eclipsed by Moomintroll/Snufkin due to the huge amounts of Ho Yay they receive. If stories that go for the One True Threesome (itself a very popular choice) are excluded, Archive of Our Own has over a dozen times more stories for the latter pairing than the former.
Nancy Drew and Frank Hardy. Judging from Fanfiction.net and multiple fan boards, these two are the most popular pairing between the two series, even though the official canon couples are Nancy/Ned Nickerson, and Frank/Callie Shaw. Within book canon, Frank and Nancy rarely interact. They are in the same 'verse, but don't live anywhere near each other and only occasionally join forces to solve mysteries, with only light Ship Tease and nothing beyond that. It's rare to see a fanfic that pairs Nancy with anyone but Frank and Ned, and Ned definitely runs a distant second place.
The Pendragon Adventure: Mark/Courtney and Bobby/Loor were both by far more popular than the canon ending pairing of Bobby/Courtney due to many fans believing having Bobby and Courtney together at the end undid a lot of both characters' character development. It didn't help that the latter pairing only came together as the result of a contradictory Reset Button ending.
Septimus Heap: Septimus/Jenna in spite of the fact that Septimus and Jenna are adopted siblings, Jenna herself is given an apparent canon love interest in the form of Septimus's best friend Beetle. Marcia/Silas as well, in spite of the fact that Silas is married and has seven kids.
A Song of Ice and Fire: Jon/Daenerys is a popular ship and has been speculated for nearly 25 years during which A Song of Ice and Fire has been published. While Jon/Daenerys becomes canon in latter seasons of its show counterpart Gameof Thrones, by that point the show had diverged radically from the books. As of the latest book, A Dance With Dragons, Jon and Daenerys have yet to meet.
Star Wars Legends had many phases throughout the 90s of writers doing their best to bury Mara Jade, Luke's closest female companion in The Thrawn Trilogy, in favor of introducing new paramours for Luke: Callista Ming, Jem Ysanna, Akanna Pell, and so on. None of them managed to land with the fandom, which stuck with Luke/Mara fervently enough that it became the Official Couple.
Despite (because of?) the lengths gone to establish Ashe as Rhapsody's soul mate, many Symphony of Ages fans prefer to pair her with Achmed.
Tortall Universe: Beka and Rosto in Beka Cooper, as she ends up marrying Farmer, who didn't appear in the first two books. And then The Numair Chronicles threw fuel on the fire by revealing that at least two of Beka's descendants were named 'Rosto'.
Many fans think that Bella would have been better off with Jacob than Edward. A lot of reviewers of the film adaptation of New Moon agreed with them, saying that Bella had more chemistry and believable development with Jacob than she did with Edward.
Jacob/Leah is also preferred over Jacob/Nessie.
Subsequently, people prefer shipping Nessie with Seth, because he's closer to her age, is a very likable guy, and a relationship with him would lack the enormous unfortunate implications and Squick Jacob/Nessie has.
Bella and Alice also have a large following due to their Relationship Writing Fumble. It also avoids pairing Bella with someone who shows manipulative and controlling behavior towards her, which both Edward and Jacob have displayed.
Even though the canon pairing is Gregor/Luxa, many The Underland Chronicles fans seem to prefer Gregor/Howard for some reason.
The Vampire Chronicles: Louis is the preferred partner for Lestat across the fandom despite Louis getting much, much less screen time than in the first few books and Lestat falling for other people left and right, such as Rowan Mayfair in the last book. This is probably why AR makes a point of having Lestat call Louis "most beloved" in later books and sulk over missing him.
The Vampire Diaries: Damon and Elena have always been a fan-favorite, despite her staying with Stefan throughout the books. This continued into the TV show, where the producers pretty much switched the endgame to Damon/Elena instead of Stefan/Elena due to the popularity of the relationship and how the flash-forward in the series finale reveals that they stayed together until they died.
Warcraft: The Last Guardian has Garona and Khadgar; so much so that when Garona was first announced to have a son with magical potential, many fans assumed the father would be Khadgar.
Lionblaze was commonly paired with Icecloud and Hazetail in fanworks, the former because she barely got any screen-time, and the latter because it was hinted that he had a crush on her. His Relationship Upgrade with Cinderheart did nothing to stop the fans.
Mothwing/Leafpool is vastly more popular than the canon Crowfeather/Leafpool, mainly since the latter was Strangled by the Red String. The former ship's sudden surge in popularity in recent years has made this even more prominent.
The Wheel of Time has Moiraine canonically paired with Thom. However, while that ship still has its fans and was generally her most popular when the books first released, in more recent years most fans have taken to shipping her with her best friend Siuan due to feeling that they have better chemistry and the fact that the two were "pillow friends" while they were younger. It certainly doesn't hurt that the 2021 series made them an Official Couple.
The Woman in White has Walter and Marian. His close, equal friendship with her and how tough and brilliant she is despite her ugliness make the couple much more interesting than his romance with the beautiful but boring and helpless Damsel in Distress Laura.
, comparing such boys to the Big Bad, and writing Fan Fiction dedicated entirely to torturing or complaining about said boys