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. Mary Jane's relationship with Peter has been mostly written out of the books, and different love interests have been brought in to be Peter's romantic partner (like Deb Whitman, or the more recent Carlie Cooper). However, Mary Jane is still popular with many fans and from the very start of their relationship, many fans have preferred Peter to be with MJ.
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 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. Then 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 the 100th issue of Teen Titans in 2011... but then came the New 52 reboot. Shoot.
Owing to a series of continuity reboots, Superman has zigzagged all over with Fan-Preferred Couple status. When the New 52 launched, for the first time in the decades-long history of the characters, Lois Lane and Superman were the Fan Preferred Couple, as he was paired with with Wonder Woman instead of his classic love interest. Wonder Woman/Superman had a staunch foundation of supporters, and furthermore had been teased as a pairing for many years, besides being an Official Couple in various Elseworlds stories. This departure from classic Superman—among others—proved ultimately to be more unpopular than not, so DC brought back the original Superman and Lois into the New 52 Universe for DC Rebirth, which saw the seeming death of New 52 Superman and Lois, only for Superman Reborn to reveal that they were still alive, that Superman and Lois were split into their pre-Flashpoint and New 52 selves, and upon the halves of both Clark and Lois remerging, and history being altered closer to the pre-Flashpoint one (including the Superman/Wonder Woman being Retgoned.
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. While both had new love interests for a long while in the New 52 there was always tons of Ship Tease whenever the two interacted, and it seemed the writers for everything the two appeared in very much wanted the two together but just weren't allowed or something. The only love interest who got even a slight degree of support was Helena Bertinelli, who was in a relationship with Dick Pre-Flashpoint, and even then it was considered nice for a temporary romance, and as part of the Fish out of Water nature of Dick's series.
Tim Drake and Stephanie Brown is by far the most favorite 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 ship tease during their very first meeting in the New-52 wouldn't be there.
Speaking of Cassandra, her most popular pairing aside from Cassandra/Stephanie (whose following, in itself, surpasses any of her canon love interests put together) would probably be with Jason Todd. In this case, it's pretty much Pair the Spares, combined with the potential intrigue of them having basically opposite personalities and both mostly operating on the edge of the Bat-family.
Bruce himself has had many girlfriends over time, yet the woman most fans want to see him with is Selina Kyle, 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.
Due his relationship with Daisy being rather rocky at best, Donald Duck has a few of these, the most notable being the one with Reginella, queen of the planet Pacificus, who he first encountered in the 1972 story "Donald Duck in the Underwater Adventure". She is considered a preferred option due her sweet nature, her tragic character, and being the one who actually has a chance (and would have already won four timeshad something not always forced their separation), and is still popular enough to have a song dedicated to her and to receive new stories once every few years.