When it comes to The Avengers, slash pairings like Thor/Loki, Tony/Loki, Steve/Tony, Bruce/Tony (or the combined Steve/Bruce/Tony) tend to be more popular than those characters with their het love interests such as Jane, Pepper, Peggy, and Betty, mostly due to the fact that those characters are nearly/completely absent from the film (or, in Peggy's case, old).
However, this only applied to The Avengers, and not to the Marvel Cinematic Universe movies that those characters originated in. But in the case of Captain America, Steve/Bucky tends to heavily rival, if not eclipse, Steve/Peggy and Steve/Tony in many fan circles. Which makes sense — Steve's relationship with Bucky is arguably the biggest overarching theme of his series of films, and by extension, his character arc.
And the Thor movies, where Thor/Sif and Thor/Loki are both more popular than Thor/Jane.
Loki/Black Widow often gets this treatment thanks to a healthy dose of Foe Yay they recieved in the film when they're not slashing Loki with the male members of The Avengers. It's enough to rival, even eclipse, fans of Hawkeye/Black Widow.
The Avengers also gives us the heavily-hinted but not outright canon ship of Black Widow/Hawkeye. Unfortunately for its fans, it was sunk in Age of Ultronthanks to The Reveal that Hawkeye is Happily Married with kids; as a result people started pairing up Natasha with either Steve, based on their strong chemistry in Winter Soldier, or Bucky, based on their canonical relationship in the comics.
Inverted. Even before the movie came out, pre-release implications that Bruce Banner and Black Widow would become a couple was met with fairly unanimous disapproval, mockery, and outright confusion from the fanbase. This is due to many reasons, namely all their interactions in the first film only showing Natasha being afraid of Bruce and him attacking her as The Hulk, on top of the two having much stronger connections with other characters, making Bruce one of the least popular partners for Black Widow. While some shippers jumped onboard and some critics even cited their relationship as one of the film’s better aspects, the overall reception to Bruce/Natasha remained mostly negative; many even likening the ship to being Strangled by the Red String.
Wanda Maximoff/Scarlet Witch is currently starting to be shipped with two people: Clint Barton and Steve Rogers. The first for the use of All Love Is Unrequited and giving her an epic speech, and the second for supporting and helping the twins and being... Steve Rogers.
Possibly as popular as the above would be Wanda/Vision, for all the Ship Tease, and the added bonus of them being a couple in the comics.
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.
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.
Some The Great Race fans consider Maggie/Professor Fate as having more chemistry than Leslie/Maggie. Probably not helped by how one hilarious 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.
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.
In the film adaptation of The Hobbit, the most popular ship among fans is Thorin/Bilbo.
There isn't much fanfiction for John Tucker Must Die but 60% are Kate/Beth and probably 39% are Kate/John with Scott being ignored.
Fans of Kick-Ass tend to prefer shipping Dave/Kick-Ass with Mindy/Hit-Girl, instead of his official love interest Katie. The sequel panders to this by making Katie into a cheating bitch out of nowhere, and featuring a kiss between Dave and Mindy at the film's end.
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. Chaucer and Wat are also a major Fan Preferred Couple.
While Mo is paired up with Scott in Lemonade Mouth, fans like to ship her with Charlie instead. Meanwhile, Stella doesn't end up with anyone, but it hasn't stopped fans from pairing her with Ray, probably due to all the Foe Yay.
Mary Poppins and Bert are this in Mary Poppins, in large part due to Julie Andrews and Dick Van Dyke's chemistry. It is even implied to be made canon in the Broadway Musical when she kisses him on the cheek.
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.
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.
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.
In Red Eye, many ship Lisa and Rippner, in spite of (or because of?) all the attempted murder on both sides, as well as the intense chemistry between Rachel McAdams and Cillian Murphy, especially during the lavatory scene.
Schindler's List has Amon and Helen, pairing occasionally supported by viewers, despite the unlikelihood of it ever possibly working out, particularly since Amon mostly seems to see her as something he likes to possess than actually caring about her.
While nothing actually happens in School of Rock, a lot of people like to imagine that Dewey and Ms Mullins dated after the Battle of the Bands. This is mainly brought on by the bar scene, where Dewey is able to get her to let her hair down a little.
This is made obvious in the stage version, where they share a kiss during that bar scene and another after the Battle of the Bands, and by the end it's heavily implied that they're officially a couple.
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 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 the Star Trek2009 movie is Spock/Uhura. There is a sizable section of the fandom for whom Kirk/Spock is the Fan-Preferred Couple, some of whom believe that the former relationship 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, only to have McCoy/Marcus develop a sizable following.
When the film came out, it did not take long for fans to start shipping Kylo Ren with Rey. Fans were intrigued by the characters' intense interactions, considering them to be much more interesting and ripe with possibilities than the potential for a Rey/Finn romance. The fact that it is strongly suggested that Kylo Ren has a Villainous Crush on Rey—he bridal carries her, watches her sleep and even volunteers to be her teacher—only added fuel to the fire. However, the ship is the source of a major Broken Base, with many other fans thinking that their Foe Yay has some parallels to an abusive relationship or theorizing that they might end up being related.
The other popular ship to come out of the film is that of Finn and Poe Dameron, thanks to their ungodly amounts of Ho Yay, such as Poe telling Finn to keep his jacket because it suits him. Poe's actor, Oscar Isaac, even implied in an interview that Poe might be romantically interested in Finn. However, Finn's actor also expressed in a separate interview that Finn/Poe was strictly a bromance. Imagine the surprise when yet anotherinterview reopened the possibility of a romance between the two, with John Boyega taking back his prior statement.
Logan/Rogue is much more popular than Logan/Jean or Bobby/Rogue, and it's actually the #1 couple of the original trilogy.
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.