A lot of people forget that Archie and Veronica were the original Official Couple; it's only because of Betty being a Better Than Canon match for him that Betty and Veronica even became a question. The newspaper comic version does a much better job of emphasizing Archie/Veronica, but this still just doesn't help at all. During the last couple of decades, the writers have tried to make the triangle more even; Betty gets about as many dates with Archie, and Veronica has several other (one-shot) boyfriends.
Spider-Man/Mary Jane. Yes, you read that right. You have Joe Quesada to thank. MJ actually has more of a history of this reaction: she was—and still is—very popular with the fans, and she's been written out of the books before to have a more "appropriate" love interest brought in to be Peter's romantic partner (like Deb Whitman, or the more recent Carlie Cooper). Problem is, with the exception of maybe The Black Cat, these love interests are as dull as a rock and don't hold a candle to MJ's character. From the very start of their relationship, fans preferred Peter with MJ. If only those silly creators didn't get in the way...
If you know where to look, Peter and MJ are still very much together (the Spider-Man newspaper strip for example)
Back when Gwen was still alive and Peter Parkers's official love interest, Mary Jane Watson's unexpectedly huge popularity with the readers was a serious problem for Stan Lee and John Romita. They tried a lot of things to tone MJ down and make Gwen more "exciting," which in some respects only lampshaded their problem as it made Gwen more and more resemble MJ, most notably by changing her original hairstyle into a variant of Mary Jane's. The way Stan Lee wrote about it later, the matter was not helped by the fact that he himself found Gwen less interesting than MJ...
In The Mighty Thor, the mightiest pairing is easily the Foe Yay/Ho Yay/Not Blood Siblings-Yay of Thor/Loki. This is most likely because they're the two most established characters in the series, and have a few really heartwarming moments that the shippers run with. Plus, on the het side, the Thor/Jane (or Don/Jane, it's gotten confusing) Thor/Sif, and Thor/Amora shippers are too busy fighting with each other to deal with Thor/Loki shippers. Even though it's canon, most people regard Doctor DoomxLoki as a joke.
Many fans prefer Invisible Woman to be paired off with Namor rather than her own husband. Considering the playing-up of Mr. Fantastic's neglectful side AND having Sue and Reed be on opposite sides of the Civil War, it seemed like a distinct possibility. (And, not surprisingly, it didn't happen. But they did tease us with it a bit.)
An interesting situation occurs in the Knights of the Old Republic comic since many fans wanted Zayne to hook up with Jarael instead of his more obvious love interest, Shel. The reason this is an interesting situation is because Zayne and Jarael become a couple in the last issue, thus making this a rare example of the Fan-Preferred Coupleturning into the Official Couple.
For a long time, X-Men Wolverine/Jean Grey was a lot more popular than the well-established, long-term Cyclops/Jean Grey. The love triangle was popular enough to persist in most adaptations of the characters, but once Cyclops hooked up with Emma Frost, and Jean Grey stayed dead for a longer time than she stayed alive, the ball was thrown back up into the air as to what was preferred.
Many Teen Titans fans were thrilled when Beast Boy and Raven got together. Than came One Year Later, during which they broke up. The fans were less than thrilled. The fandom rejoiced when the two finally grew up and reunited in 100th issue of Teen Titans in 2011... but then came the New 52 reboot. Shoot.