The Phantom of the Opera: A vast majority of 'phans' prefer the Phantom and Christine to Christine and Raoul.
The sequel Love Never Diesderails Raoul into an alcoholic, emotionally neglectful husband just to raise the possibility that the Phantom and Christine can be an official couple. It's revealed that she always loved the Phantom more all along, and they are the official couple at the end.
George Bernard Shaw was annoyed by fans of his play Pygmalion trying to ship Eliza Doolittle and Professor Higgins, and adamantly declared that the two would never be more than friends (and not very close friends, at that) and declared that, after the events in his play, Eliza Doolittle eventually marries Freddy and they open a flower shop together. He wrote an essay about that, which was included in the 1916 print edition of the play. The musical My Fair Lady, made after Shaw's death, has an ending that implies much more strongly that the two of them do get together. As Pygmalion was written in 1913 and the first film adaptation was made in 1938, this particular Fan Preferred Couple is Older Than Television.
Les Misérables: A large portion of fans seem to believe that Eponine is a better match for Marius than Cosette. Admittedly, Cosette doesn't do much in the musical besides hit a B flat and flirt with Marius.
In a lot of respects, that suits Victor Hugo's purpose well: Eponine's role in the original novel was a commentary on the unfairness of class distinctions in contemporary French society, which meant that Eponine/Marius was not 'proper'.
And now there are many fans who think that if Eponine got over Marius, she and Enjolras would be a perfect match. Never mind what Hugo has to say, and what is described pretty well in the musical and the movie regarding Enjolras' non existent romantic life.
Enjolras/Grantaire would be this if they weren't already practically canon.
Valjean remains a Celibate Hero throughout all versions of the story, but that doesn't stop the numerous fanfics that pair him with FantineorJavert.
Elphaba/Glinda, from Wicked, is more popular then the other couples such as Fiyero/Elphaba.
Personally that's debatable, this troper's experience is that there's a lot of fans who ship Fiyero/Elphaba too, the fans of the respective ships deal with the fact half the fandom don't support their ship by pretending the other kind don't exist.
Tracy/Seaweed from Hairspray, rather than Tracy/Link, particularly due to the 2007 film, where Link's role of actually helping Tracy is cut and it's generally felt he did nothing to earn Tracy in the end other than feel sorry about his actions.
Starlight Express fans are more likely to pair Electra's minions with each other or with other trucks than with Electra himself. Wrench/Volta and Purse/Caboose are probably the two most popular ships.
There aren't that many Alfred/Sarah shippers out there. Most Tanz der Vampire fans seem to prefer Sarah with Krolock, and a strong number like to pair Alfred with Herbert. Anyone who's seen the film beforehand ships Krolock/Professor with renewed vigour, some fans going so far as to state that 'Gott ist tot' is aimed at the Professor, not Sarah.
