From Questionable Content, Jeph Jaques is on record saying that Martin and Faye were the official couple for the first 500 strips or so; however, before it visibly materialized, he changed his mind (later saying in the comic that they would have been a terrible couple) and delivered a Wham Episode that got rid of Martin/Faye and set up Martin/Dora. He later paired Faye up with Angus McPhee. However, he then broke up Marten and Dora and put Marten together with Padma, a new character, only to reveal that Padma would be leaving soon to California to take care of her mother. Faye then broke up with Angus leaving the current offical couples as Marten with Claire, Dora with Tai and Marigold with Dale.
El Goonish Shive has three: Tedd/Grace, Elliot/Sarah ( formerly ) and Ellen/Nanase.
Homestuck has Dad Egbert / Mom Lalonde. They even have a romantic dinner together. Then they die. Their Official Couple status is cemented in this update explaining the Troll Romance Quadrants, where they're given as the paradigm for "matesprits" the closest parallel to human romance that Trolls have. Later on, Spades Slick and Ms. Paint. Despite implications that he used to have a thing for Ms. Paint himself, Hussie decides not to come between them and declares their ship canon on the spot. And of course, there's Rosemary (that's Rose and Kanaya, the portmanteau comes from Kanaya's last name, Maryam), seemingly a favorite of the fandom and now official!
Persona 4TW originally had MC/Rise; however, Persona 4TW Add-On had them break up, and Gold'n Persona 4TW (which takes place in between the two) shows the cracks that led to them breaking up, and also indicates that MC/Marie will be the official couple in the future.