Batman v Superman: Dawn of Justice: Despite Clark Kent being in a loving relationship with Lois Lane, most fanfiction about the film, and the DC Extended Universe as a whole, instead pair him up with rival turned ally Bruce Wayne. This is due to the Foe Yay between them throughout the films, as well as the fact that the pairing already being popular in the comics. This only grew after Justice League (2017), where Bruce spends much of the movie trying to revive Clark and ranking up the Ho Yay between the two. They have the most fanfictions of any pairing in the DCEU tag on Archive of Our Own.
Bill & Ted has, well, Bill/Ted. The fact that their actual girlfriends qualify as Satellite Love Interests helps. Most fanworks for the film tend to be for the ship, especially on Tumblr.
Forget the fans, even the haters agree when it comes to The Book Of Masters. Yangul/Katya is vastly preferred over the Official Couple Ivan/Katya. Yangul has several poignant I Want My Beloved to Be Happy scenes with Katya and shows readiness to make sacrifices for her sake (culminating in a full-fledged Heroic Sacrifice). Meanwhile, most viewers think Ivan and Katya barely get any chemistry and Ivan just gets bonus after bonus thanks to their relationship.
While fans have enjoyed going into the various alternate pairing ideas for The Breakfast Club, Bender/Allison is clearly the most popular. Due to how both Bender and Allison are quite the outcasts, Bender/Allison fanfics have a known tendency to give them a Birds of a Feather dynamic. Though to be fair Bender's line to Allison early in the movie "I've seen you before you know" has been occasionally used as Fanfic Fuel.
Bring It On: Most of the fans of the first movie pair Torrance with Missy instead of her brother Cliff. This is due to their friendship that is littered with heaps of Les Yay, as well as Torrance really wanting Missy on the team and the two instantly hitting it off. Also, many fans feeling that they have better chemistry than her with Cliff. On Archive of Our Own they have the most fanfiction of any ship from the film series.
Cadet Kelly: Despite Kelly having a crush on Brad, many fans prefer to pair her with Jennifer. This is due to the intense Foe Yay and Les Yay between them. As their rivalry and eventual friendship drives the plot of the movie to the point that a ribbon dance between the two is the climax of the film and their goodbye at the end is strangely poignant. Meanwhile, Brad fades out of focus through the film. There's not much fanfiction about the film, but if you find one it's usually a Kelly/Jennifer one.
Many fans prefer to ship Nate with Caitlyn over his canon girlfriend Dana, despite the two barely interacting with each other in either movie. This is due to the feeling that their personalities would work better together than Nate and Dana.
On Fanfiction Dot Net, the number of crossover fics that pair Mitchie with Alex Russo rival or even surpass those that pair her with her actual boyfriend Shane, likely due to fans feeling their personalities would work well together and the real life relationship between theiractresses. These fics tend to either be the two meeting in a canon-like situation or complete AUs that reinvent both settings from the ground up.
Fans of the Rupert Grint movie Cherrybomb can generally be split into two categories: devoted Malachy/Luke shippers who simply ignore Michelle's existence; and batshit crazy, foaming-at-the-mouth Malachy/Luke shippers who openly detest Michelle and loudly wish her dead. This is a pretty extreme reaction given that in canon, both guys are seemingly straight and spend most of the movie competing for Michelle's affections. That said, several cast members have alluded to the strong homoerotic subtext of Malachy and Luke's relationship, so it probably doesn't exist entirely in the minds of yaoi fangirls.
The Craft: Sarah and Nancy is the most popular ship in the fandom. It doesn't help with Nancy's Ambiguously Bi moments, her obsession with Sarah, and the fact that Sarah's Love Interest, Chris, is a sleazy asshole who mistreats her.
Descendants: Mal/Evie is more popular than Mal/Ben or Evie/Doug. This mainly due to the Les Yay between them over the course of the three movies. Many fans feel that the two had better chemistry with each other then they did with either of their actual boyfriends. Such as the scene where Evie is complimenting Mal's appearance in the mirror with her head on Mal's shoulder. Their duet Space Between also got many to jump on board ship. They have the most stories about them together on Archive of Our Own.
The Devil Wears Prada: Most fans of the film adaptation prefer to ship Andy with Miranda over her canon love interest Nate. Reasons for such seem to be Meryl Streep's seductive performance, and feeling that they better chemistry then Andy did with Nate. (It helps that Nate is pretty much The Scrappy.) As well as the fact that their growing relationship drives the film and the Foe Yay between the two. The fanfiction about the two being in the 2000s on Archive of Our Own, and it remains quite popular on sites like Tumblr and YouTube to this day.
Rahul and Nisha from Dil To Pagal Hai have a following, if only because Pooja is sometimes considered TOO perfect...
Fans of An Education like to pair Jenny with Danny, especially since her love interest in the film is married.
Fans of the Brit Com film Four Weddings and a Funeral often complain that the main character's witty, lovelorn friend Fiona is a far better match for him than the vacuous American he ends up with.
Ghostbusters (1984): Despite Janine ending up with Louis in the second movie, most fans don't ship her with him. Instead, most fans preferred her awkward chemistry with Egon. This is also helped by the fact that she had a crush on him in the original and the cartoon having Ship Tease between the two. Egon's actor and franchise co-creator, Harold Ramis, hated the two together and had the romance dropped from the second one. Still most fans prefer to ship them together, over her with Louis. With the pairing being the most popular ship from the original movies on Archive of Our Own.
Ghostbusters (2016): Jillian Holtzmann/Erin Gilbert is by far the most popular pairing from the film. This is partly thanks to a combination of the "Rhythm of the Night" sequence, a deleted scene in which Holtzmann declares she and Erin are dating, and Holtzmann being the films Breakout Character while Erin is the lead. Holtzmann's actress Kate McKinnon has also openly described her as flirting with Erin in their first meeting.
Some The Great Race fans consider Maggie/Professor Fate as having more chemistry than Leslie/Maggie. Probably not helped by how one scene has her actually kissing the guy. There's actually some Reality Subtext here. Natalie Wood was forced by the studio to do this movie against her wishes, then to make matters worse she was paired up with Tony Curtis. They'd already done two films together and had developed a passionate hatred for each other, so the lack of chemistry between Maggie and Leslie was genuine.
After all the strife Harper put Abby through in Happiest Season, quite a number of viewers expressed a desire to see Abby get together with Harper's ex Riley instead, including Rileys actress Aubrey Plaza.
High School Musical fans have been shipping Chad and Ryan ever since the second movie. Ryan's "You'll never know if you never try" and Chad's "I'll show you how I swing" have served as innuendo, while wearing each other's clothes fueled additional locker room images. Chad's relationship with Taylor and Ryan's Love Interest Kelsi (added in the third movie) have not deterred shippers the slightest. Chad/Ryan seem to be more popular than series Official Couple Troy/Gabriella, with Archive of Our Own featuring four times as many tags for Chad/Ryan than for Troy/Gabriella.
Johanna/Finnick became quite popular as well, especially since Finnick's canon Love Interest Annie is barely seen and mostly exists just to be a Satellite Love Interest to Finnick. It helps their actors had great chemistry, especially in Catching Fire and both characters are very active members of the rebellion.
Jennifer's Body: Most of the film's fandom ships Jennifer and Needy together. Other ships are basically nonexistent. This is mostly due to the huge Les Yay and Foe Yay between them. To the point that it's barely subtext. Even Megan Fox said she played Jennifer as a lesbian with a crush on Needy. On Archive of Our Own and Fanfiction Dot Net this pairing has the most fanfiction of any other pairing. Needy/Chip barely has any on either website, however he does manage to avoid Die for Our Ship.
John Tucker Must Die: Despite Kate ending up with Scott, most fans don't ship her with him. Instead most fans prefer to pair Kate with Beth. This is usually due to the fact that they actually kiss, Beth often being interpreted as bisexual, and the chemistry between the two actresses. There's not much fanfiction about the film, but most of it is Kate/Beth.
A lot of fans of A Knight's Tale aren't fond of William/Jocelyn, instead preferring to hook him up with his hard-working friend Kate.
While Mo is paired up with Scott in Lemonade Mouth, fans like to ship her with Charlie instead.
Live Free or Die Hard: While John McClane had his tumultuous marriage to Holly in previous movies and Matthew Farrell has his budding romance with Lucy in this one, fans expressed far more interest in McClane and Farrell getting together due to the movie being centered around their dynamic and Bruce Willis and Justin Long having good chemistry too. Most of the fanfiction about the film series as a whole is John/Matt.
The Lost Boys: Michael's canon love interest is Star, but you wouldn't think so with all the fanfics pairing him with David. This is mostly due to the Ho Yay and Foe Yay between the two, as well as the fact that David often gets the Draco in Leather Pants treatment from fans due to being played by Kiefer Sutherland. On most sites like AO3 or Tumblr, Michael/David dominates the shipping for the series.
Maleficent: Maleficent/Aurora has a much bigger following than Aurora/Phillip, though this is the most popular ship only for Aurora and not Maleficent.
Mamma Mia!: In the film adaptation, Rosie has a crush on Bill and eventually gets with him in the climax of the movie. They break up sometime between movies, but get back together in the second one. However, most fans prefer to pair her with Tanya. This is due to it being hinted that Bill cheating on her being the reason they brook up and the Les Yay between the two. On Archive of Our Own, the fanfics about the two together even outnumber the ones featuring the canon pairing, Sam/Donna.
Mulan (2020): Mulan/Xian Lang almost instantly became a popular pairing, and is easily more popular than Mulan/Chen. Reasons why are Xian Lang's attempts to seduce her to the dark side, she even tenderly strokes Mulan's sword and brushes her hair out of her face while they fight. Xian Lang even sacrifices herself to save Mulan and dies in her arms. Their dynamic is seen as one of the few good things about the movie by many. As well as, Xian being a fan favorite, while Chen being seen as Replacement Scrappy for Li Shang.
A chunk of the Now, Voyager audience seem to prefer Dr Jaquith as a romantic partner for Charlotte, finding Jerry a little dull in comparison to the charming Jaquith. Bette Davis herself said that she imagined Charlotte marrying Dr. Jaquith after the film ended, as Jerry was 'too weak' for Charlotte.
Danny/Rusty is more popular than Danny/Tess is. Due to the Ho Yay between the two. As well as the fact that George Clooney and Brad Pitt have better chemistry than Clooney with Julia Roberts. Together they make up the most popular pairing of the trilogy.
Debbie/Lou from the spinoff Ocean's 8 is easily more popular than Debbie/Claude. This is mostly the huge amount of Les Yay between the two. Such as when after Debbie gets out of jail, Lou greets her with a kiss, as well as the great chemistry between Sandra Bullock and Cate Blanchett. They have the most fanfiction about them on Archive of Our Own, even topping Danny/Rusty.
Raoul and Christine end up together in The Phantom of the Opera, but most fans prefer Christine to be with Erik - especially the ones that go by the 2004 version of it (where the Phantom is portrayed by Gerard Butler). Also see the series' entry in the Theater section.
Ever since the trailer for Pitch Perfect (before the characters even had names) came out, people latched onto Beca/Chloe. Jesse never stood a chance and his creepy behavior towards Beca in the movie proper didn't help matters.
Rosie/Carter is the most popular ship for Princess Protection Program. This is due to the great chemistry between Selena Gomez and Demi Lovato. As well as their well-developed friendship that is the emotional center of the film. It's rare to find a fanfic with either ending up with Ed or Donny. Most of the canonical fanfiction (as opposed to ones based on Selena and Demi which are slotted there falsely at times) are about the Princess and the Bait girl living happily ever after.
In Push: Compare Nick and Cassie's number of YouTube videos (over twenty) to Nick and Kira's (none). Yeah.
The Queen of the Damned fandom in general favors the vampire/vampire pairing Lestat/Akasha over the human/vampire pairing Lestat/Jesse. This despite Akasha being portrayed as pure evil and a bloodthirsty megalomaniac who wants to drink the world dry, Akasha had Evil Is Sexy going for her while Jesse was made into a Damsel Scrappy and mousy Vampire Vannabe who just got on viewers' nerves.
Ready or Not (2019): While Grace is married to Alex, many fans prefer to pair her with his brother Daniel. This is because Alex ends up betraying Grace and sides with his family over her, while Daniel goes out of his way to assist her and even performs a Heroic Sacrifice to give her some more time.
She's the Man: Most fanfiction about this film on Archive of Our Own has Viola and Olivia ending up together rather than with their respective love interests, Duke and Sebastian. This is mostly due to flirting and build-up occurring between them rather than between Olivia and Sebastian. It also stems from fans feeling that Viola and Olivia have more chemistry than Duke and Viola.
Fans of Snow White and the Huntsman prefer Snow White/Huntsman as opposed to Snow White/William. It does not help that the Huntsman kissing Snow White is what awakens her from death after eating the poisoned apple, whilst William's kiss did nothing, carrying the implication hes her One True Love, but in the sequel shes married to William and the Huntsman ends up back with his Not Quite Dead wife, Sara.
Speed: Jack Traven and Annie Porter, though they've split up between this movie and the next one, still get a lot of support from the fans given not only how loved this movie is and how reviled the sequel is, but also given both the very well-received chemistry between Keanu Reeves and Sandra Bullock and that Annie's new Love Interest Alex Shaw (Jason Patric) is essentially just a less-interesting Expy of Jack.
In the DVD commentary for Starship Troopers, director Paul Verhoeven says fans wanted Carmen to die and Johnny to end up with Dizzy, proving that it isn't only fans who have preferred couples. Considering that in the original book Dizzy is male (not to mention dead for a good chunk of the book) and Johnny and Carmen have at most a one-night stand together, this wouldn't have been such a bad change compared to most of the rest of the changes Verhoeven actually did make.
The Official Couple in Star Trek (2009) is Spock/Uhura. There is a sizable section of the fandom for whom Kirk/Spock is the Fan-Preferred Couple, a carry over from the original TV series where Kirk/Spock was vastly more popular than any other ship, and some of them believe that Spock/Uhura was put in purely to dissuade Kirk/Spock shippers. In the second reboot movie they introduced Dr. Carol Marcus as Kirk's potential love interest.
Star Wars: Finn/Poe was initially the sequel trilogy's most popular pairing overall thanks to their shippy interactions in The Force Awakens. Although an official love interest for Finn was introduced in the form of The Last Jedi's Rose Tico, and The Rise of Skywalker introduced Jannah and Zorii Bliss seemingly as Implied Love Interest figures for the two, it's still easily the most popular pairing for both characters and the characters' actors have expressed their support of it in interviews.
Most Teen Beach Movie fans seem to prefer pairings Lela and Mack together over their canon pairings with Tanner and Brady. They have the most fics about them on Archive of Our Own. Reasons why may include their Les Yay in the films or their expanded relationship in the second movie that is hinted to have survived the 53 years of history reset.
Top Gun attempts to sell Maverick/Charlie as the Official Couple, however very few people really buy into it, pointing out that there's more chemistry between Maverick and his best friend and Guy in Back Goose. The way they interact with one another is very akin to a married couple, and when Goose dies, Maverick's subsequent mannerisms seem very much like that of a widow. In contrast, Maverick and Charlie get intimate in scenes that don't really seem to tie into the overall plot and themes.
This happens in-universe in The Truman Show, where it's revealed that Truman's wife, Meryl, is rather unpopular among the audience—she's not a great actress, quite a few of her lines are Product Placement, and her attempts to show that she loves Truman are way too over-the-top to believe. Instead, Truman seems drawn to Sylvia, his old high-school flame, whom he had a much better connection with but who was written out of the show because she tried to tell him the truth. It's suggested that the audience actually agrees with Truman, thinking that him and Sylvia had better chemistry and calling Meryl "the rebound."
Ryan and Natalie from Up in the Air, mostly due to the fact that in the final act it's revealed Ryan's love interest, Alex, is married with a family.
Venom (2018): Eddie/Venom has become incredibly popular amongst the fandom, being paired up together constantly despite Venom being an extraterrestrial blob of tar not confirmed capable of sexual reproduction. Reasons why tend to be their dynamic being seen as the best part of the film, the fact that they actually kiss, though Venom was bonded with Anne at the time, and the fact that their bonding is the emotional center of the film. It is incredibly popular on Tumblr and other fanfiction sites, and easily tops the canon Eddie/Anne.
After the release of the first movie most fans found themselves shipping Logan and Rogue together instead of their canon ships of Jean and Bobby respectively. This mostly due to their growing relationship being a main focus of the movie and Rogue having an unrequited crush on Logan. Even after Logan gets multiple love interests and dies in his solo films, Rogan still outshines every other film pairing besides Charles x Erik. (It helps Rogue is one of the few women who is romantically teased with Logan who doesn't die afterwards.)
Charles/Erik is the official pairing in X-Men: First Class, even according to certain screenwriters and actors. It's incorporated even in fics that involve the younger X-Men (by having them act as parents), and those who do ship Erik/Raven or Charles/Moira are a small minority. Charles/Erik even managed to supplant Logan/Rogue as the most popular pairing of the film series—just look at the difference in the sheer number of stories on Archive of Our Own for proof. James McAvoy wasn't kidding when he called it the "Brangelina of X-Men"; Cherik has become such a phenomenon that British TV host Graham Norton took notice of it and showed McAvoy and Fassbender some of the fanart and fanfiction. On the other side of the pond, Conan O'Brien's interview with the two actors was almost exclusively about their onscreen/offscreen Ho Yay, and a Cherik fanvid was screened at the end.