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...
Gwen is pretty much the only one of Peter's love interests who's even been popular enough to even merit comparison to MJ, and she's been dead for decades, and she was still always a distant second from pretty much the instant MJ was introduced. She's still second place after all this time, well behind MJ but way ahead of every single MJ replacement that Marvel has tried to trot out. Yet the people in charge still don't get the message about who Spidey fans want him paired with.
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 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.
Like many other comic book examples, Rogue and Gambit used to be an item, and after the writers split them up in the '00s they continued to be preferred by the fans. Usually one of the first questions a new writer for one of these characters gets is "Are you going to hook them back up yet?".
While subject to almost as much Ship-to-Ship Combat as her daddy, the majority of fans of X-23 still resent Marjorie Liu splitting up X and Hellion during the Baby Sitting arc of her solo series, and mentioning that arc is certain to cause much gnashing of teeth. Especially after Brian Michael Bendis hamfistedly tossed her together with O5!Angel, despite them having had no prior interaction before he hooked them up.
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.
Since the reboot of the DC Universe in the New 52, Superman and Lois Lane are now the Fan-Preferred Couple for the first time in their decades long history, having always been the Official Couple in mainstream works. Superman is currently with Wonder Woman, but you can see the sharp divide in writers and staff at DC between who prefers which girl better—various issues play up or play down Clark Kent's relationship with Lois as preferred by the writer. For the fans at large, most still see Lois as the "real" love interest.
The Batman franchise has numerous couples that fans prefer.
Almost all fans love DickGrayson and BarbaraGordon together (excepting the Dick/Starfirefanbase, that is). They've gone back and forth between being canon or not, but usually the two are incredibly close. Given the recent directions of their respectivebooks, however, it's unlikely they'll cross paths anytime soon. However, DC's upcoming Convergence event seem to be favoring the pre-52 versions of the pair with a mini-series dedicated to the couple (and, cherry-on-cake, it's written by Gail Simone).
Tim Drake and Stephanie Brown is by far the most favourite pairing for these two characters. Even Cassandra Cain can't keep up with that. The fans had decided about this very early in Tim's own series and any attempt to get different pairings was doomed to failure. The writers are clearly aware of this, otherwise the shiptease during their very first meeting in the New-52 wouldn't be there.
Bruce himself has had many girlfriends over time, yet the woman most fans want to see him with is Selina Kyle, the Catwoman. There of course is frustration whenever writers fumble it up. Notably, the Golden Age versions of them were together and even had a daughter, Helena Wayne (the original Huntress), who has endured in the mainstream comics in spite of anything else that happens.