Agent Pendergast has Pendergast/Corrie, Pendergast/Diogenes, Pendergast/D'Agosta, Pendergast/Constance...
Alice and the Mad Hatter in Alice in Wonderland. The original book is for children, but some adaptations and sequels gave their relationship romantic traits. Naturally, Alice/Hatter is now the most desired ship.
And at Disneyland, two of the costumed actors who play them are actually in a relationship, and therefore the Disney incarnations have a pretty big following on sites like Deviantart as well.
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.
Artemis/Holly in Artemis Fowl has been the Fan Preferred Couple since the very first book. Even when Holly HATED Artemis.
Which takes MayflyDecember Romance to an extreme because not only is Holly very long-lived, but Artemis began the series as a prepubescent child.
The Heroes of Olympus: Despite Reyna having unrequited feelings for Jason, most fans prefer to pair her up with his sister Thalia. This is in spite of how little they interacted together, Thalia being a Hunter of Artemis, which means she can't have any romantic relationships, and that they first meet when Thalia, along with the rest of the Hunters, technically kidnap her. However, due to the two's surprising chemistry, and the fact that they hit it off really well in a short amount of time, the ship took off, even overtaking Thalia's other popular ship with Luke on Archive of Our Own. This even gets referenced in The Trials of Apollo, where Apollo wonders if they are dating due to how close they are.
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. 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.
The 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.
An odd example with Mary Renault's The Charioteer. Laurie and Ralph end up together, so they're actually canon. However, this was not intended as an unmitigated happy ending — almost none of Renault's endings are. Many fans, particularly the straight female fanbase though also some in the gay male fanbase, think that Ralph was supposed to be the right guy for Laurie all along, when in fact Renault wrote in a letter that at the end Ralph was "being taken on out of pity" by Laurie.
Apparently, the most preferred partners for both Edmund and Lucy in the Chronicles of Narnia category are probably each other. The same for Peter and Susan. Caspian and any of the Pevensies is also extremely popular. Eustace/Jill and Polly/Digory are pretty popular as well, even though they're Platonic Life-Partners.
With Samuel Richardson's epistolary novel, Clarissa, readers wrote to the author before the last volume was released, asking him to give the story a happy ending involving a wedding between the heroine, Clarissa, and the villain, Lovelace. Readers liked Lovelace despite his actions, which included raping the main character, and thought Clarissa was prudish and a tease. Richardson not only refused to change his plans for a tragic ending, he also rewrote parts of the novel for later editions adding 200 pages and making Lovelace even more of a villain. Some readers were so against the tragic ending of the story that they wrote their own versions. Two examples of these shippers are Lady Bradshaigh and Lady Elizabeth Echlin. While Bradshaigh just rewrote the ending, giving Clarissa and Lovelace a wedding on his deathbed, Echlin rewrote her own version of the entire novel.
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.
Given that the Discworld series comprises 41 novels, and most of its Loads and Loads of Characters appear across multiple books, it's hard to single out a single pairing as the most popular. But one that is noteworthy is Mal/Polly — which has managed to make it into the top three pairings on Archive of our Own despite the two characters only appearing in a single book.
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.
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, 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). To this day, any page on this very site describing shipping or fanfic-related phenomena or reactions (Ship Mates, Die for Our Ship, Relationship Writing Fumble) will prominently mention it, and it (along with the considerably less supported Draco/Hermione) 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 having 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 together and that Harry and Hermione were (in her own words) "in some ways, a better fit."
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.
Eddie and Richie from It tend to be paired up, especially since the 2017 film.
Many readers of Ivanhoe 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 doesnt 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 cant 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.
Pre-television example in Little Women 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.
Alcott had her own reasons for this. Her father had high ideas and forced the family to live in a commune and try and be self-sufficient while he played philosopher all day. In order to prevent her family from starving, she wrote Little Women which actually was only the first half of Little Women as we know it today. It was a great success and so her publishers pushed her for another. Fans particularly pressured her to find husbands for the little women, and to get Jo and Laurie together. However the book was very much based on Alcott's own family, with Jo based on herself. Alcott wanted Jo, like herself, to remain an independent unmarried woman who earned her living through writing. However, with her family still starving, she had no other choice but to write the sequel Good Wives, but refused to let Laurie and Jo get together.
Meanwhile in the continuing sagas of Little Men and especially the latter Jos 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.
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.
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.
Enjolras/Grantaire also have a huge fanbase.
In Agatha Christie's 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.
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.
Helen (the Queen of Eddis) and the Magus of Sounis are this for some The Queen's Thief fans. Some are still happily shipping Helen/Sophos encouraged by the latter's mysterious disappearance.
Septimus Heap: Septimus/Jenna and Marcia/Silas, in spite of the fact that Septimus and Jenna are siblings and that Silas is married and has seven kids.
As of The Dying of the Light Valkryie outright states she loves him, causing Valduggery shippers everywhere to go completely nuts. However, its not overly clear if she meant it in a romantic way or platonic way. Either way, shes eighteen at the time, so it removes the issue of her being underaged.
Despite her having two canon lovers, the majority of the fandom of The Sookie Stackhouse Mysteries are rooting for Sookie to end up with either her boss, Sam the shape-shifter, or Bill's "boss", Eric Northman.
Eric Northman became the latest canon relationship. (They'd had sex before too.)
That relationship eventually falls apart as well. By the epilogue, Sookie is happily married to Sam.
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. Possibly subverted in that Achmed has decided to wait to get with Rhapsody until after Ashe dies making the couple borderline canon after all.
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.
Even though the canon pairing is Gregor/Luxa, many The Underland Chronicles fans seem to prefer Gregor/Howard for some reason.
The Villains Series has no real romance (aside from Eli and Angie in the backstory, and his sexual relationship with Serena in the first book), but the vast majority of the fandom has taken the mutualobsession between Eli and his nemesis, Victor, and run with it. The fact that they are hopelessly fixated on each other and understand each other like nobody else certainly helps.
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.
Jayfeather/Briarlight. The fact that both of them are disabled yet determined to help their Clan, along with how she moved in with him after the accident that paralyzed her, quickly caused them to become one of the most popular pairings in the fandom. The fact that Ship Tease is thrown their way like water on a fire doesn't help (or does, depending on your point of view).
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 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.