Ares, Greek god of war, had been since The Silver Age of Comic Books nothing more than a lesser enemy of Hercules and Thor who nobody cared about. Then he got a mini-series in 2004 that strongly revamped his character, and later joined the Avengers. Since then multiple writers in multiple titles were working hard to make him win the fans' love. They succeeded so much that his death caused a backlash much stronger than the death of Wasp, founding Avenger.
Blade of the Marvel comicThe Tomb of Dracula. He was the token minority character in that 1970s comic and appeared periodically to assist Quincy Harker, Frank Drake, and Rachel Van Helsing. Blade notably teamed up with vampire detective Hannibal King to defeat their archfoe Deacon Frost. He, Frank Drake, and King would continue years later in various 90s comics such as Nightstalkers and Midnight Suns. Drake would vanish as a result of Chuck Cunningham Syndrome and even Dracula himself has no reason to show up unless it's for another melee with Blade. King would show up periodically but all vampire-centric Marvel stories of the 90s and 2000s seem to acknowledge Blade as their central main character.
Bob, Agent of HYDRA became quite popular for no particular reason when he first appeared in Cable & Deadpool and has gone on to become a fan favorite. Fan reaction to his appearance in Deadpool's solo title can be summed up as, "OMG, IT'S BOB!" And of course, Deadpool being Deadpool, he knew this, even pointing out there might some day be a "Bob, Agent of HYDRA mini". Heck, Deadpool himself was only an Expy of DC's Deathstroke. His wacky nature and complete lack of fourth wall have now earned him his own series. When X-Men Origins: Wolverine was announced, his appearance was probably one of the ones people were most excited about. And after it came out? Probably the most annoyed about.
Obadiah Stane/Iron Monger from Iron Man. Between his debut in issue 163 and death in issue 200, he stands as one of the villains that managed to mentally screw up Tony Stark. You'd have to be a Darkhorse if you're the Big Bad of the first movie, despite your rather short time in the series.
Kid Loki from Journey into Mystery is pretty popular. Even after it's revealed that his entire life was essentially a "Shaggy Dog" Story, and his older self takes control of his body, he remained a very popular character. This lead to Loki gaining a role in Young Avengers, where the Kid Loki persona haunts Loki's subconscious. This, combined with MCU Loki's popularity, led to Loki getting his own ongoing series, Loki: Agent of Asgard.
And that Asgardian Agent story gave us Verity Willis, who is the perfect foil/friend for the trickster god, and also legitimately awesome in her own right.
Then, we have the other Ms. Marvel, Kamala Khan. Teenager? Check. Minority? Check. Taking up the title of an abandoned identity? Check. No major connection to the previous character? Double check. Being pushed for some sort of initiative? The whole building up the Inhumans bit - Check there. Had this been the 90s, there would have been a major uproar and demands for Carol to return to her old name. However, Kamala, who is pretty much One of Us and a sweet and lovable girl, won people over instantly with her crazy adventures and out-and-out squeeing over seeing her heroes. Her popularity exploded to the point where, not only is she part of the Avengers in the All-New, All-Different Marvel initiative, but she'll also show up in Avengers, Assemble! and Lego Marvel's Avengers (It helps that she appeared a couple of years after Carol's becoming Captain Marvel, which was itself well received).
The Runaways, while kind of a group of Ensemble Darkhorses, have three big ones. Molly Hayes, being Badass Adorable incarnate, is pretty popular. Gert is also extremely popular, with the majority of fans wanting her back on the team. The biggest would be Nico Minoru - she started as the Love Interest of Alex, but quickly caught fans' interest. Since Alex's death at the end of the first series, she took over the leadership of the team, was the first member of the team (and second teenage superhero after X-23) to appear in Marvel: Avengers Alliance and her death in Avengers Arena caused so much backlash that Marvel was forced to release a preview from the issue with her resurrection a week after, to calm fans down, skipping over the preview of an entire issue in the process.
Spider-Man himself started out as one as his first issue was expected to not sell. Expectations were proven wrong and Spidey not only got his own series but also got a franchise based around him and is generally regarded as the flagship character of the entire Marvel Universe.
The Green Goblin started out as a typical, albeit mysterious villain who was quickly considered Spidey's greatest foe even though Stan Lee almost decided not to use him as a Spider-Man villain. He was killed off and turned into a Legacy Character, eventually getting brought back simply to resolve the highly disliked Clone Saga. After Spider-Man brought him into the mainstream and he was moved to the Thunderbolts, he quickly became iconic and popular. He moved on from a Spidey foe to the star of a major comic book event. Not only that but as a result, Norman Osborn, a Villain with Good Publicity, headlined THE Top Selling Comic Book for a YEAR. Even some of his haters started to get fond of him in Superior Spider-Man as the Goblin King. He also inspired other Goblins such as Hobgoblin and his own son Harry.
Theres also Mary Jane Watson, who was originally simply meant to be The Rival of Gwen Stacy but eventually became Peter's true love
Black Cat transformed from a simple bank robber to a romantic love interest and even crime-fighting partner.
Shocker while regard as a silly for many years has also become pretty popular due his unique (quilted) design, personality, and weapons.
Hobgoblin Rodrick Kingsley is considered to be the true Hobgoblin and readers were quite pleased to see his return.
Flash Thompson as Venom got his own series and is not quite well known as Brock-Venom still is considered a runner
Venom: the black suit and Eddie Brock is also very popular as well as Carnage. Word of God is that Eddie Brock was originally slated to die after a number of issues, with the Venom symbiote bouncing around to other characters. Eddie proved so popular that he kept the symbiote much longer than planned and has stayed alive and revamped to be more of an Anti-Hero, with Carnage created specifically to fill the "evil symbiote" role originally planned for Venom.
Toxin is also quite popular; a pity that Patrick Mullgan died and that Toxin is now bonbed to Eddie Brock.
J Jonah Jameson when he's written right.
Mania from the Venom book is also quite surprising popular due to her background and design.
Mr. Negative and Overdrive are the only Brand New Day villains to stay.
Karn the only good member of the Inheritors that is actually liked by fans largely for his tragic backstory, fun design, and especially for betraying theother Inheritors.
Ben Reilly as the Scarlet Spider.
Kaine as the eventual and deeply reluctant successor to that name, who was Rescued from the Scrappy Heap by Christopher Yost, whose Scarlet Spider (2012) series became a cult hit thanks to its fun cast (including AdorkableBreak Out Character Aracely) and Kaine trying to be a hero while acting in some of the most irresponsible ways possible and dealing with the Other and the various totemic aspects of his powers that Peter had to handle in the early 2000's. While it was cancelled, Yost took Kaine and Aracely and made them the centrepiece of his New Warriors reboot. And while that was cancelled, Kaine then starred in Spider-Verse, before a Scarlet Spider who is almost certainly him (he has the same costume, same powers and same attitude) started starring in Ultimate Spider-Man. Not bad for a character who was mostly dismissed as one of the worst parts of the trainwreck that was the Clone Saga.
A lot of the new supporting cast members introduced by Dan Slott but especially Max Modell (for being a great Smart Guy for the Spiderfamily) and Anna Maria Marconi (for being really nice and her dwarfism being treated with impeccable good taste.
Sophia Sanduval from the Marvel Adventure Spider-Man. Generally down to earth, sweet, supportive of Peter/Spidey and a generally likable and entertaining companion a lot of people consider her one of Peter's best love interests behind only Mary Jane and Black Cat. So much so that when the series was eventually cancelled the biggest lament was that there would be no more Chat.
Spider-Gwen, the Gwen Stacy Spider-Woman that showed up in the storyline Spider-Verse. Fans were already clamoring for more of her just by the cover to her first official story. It got worse when previews started coming out. It was so bad that there were already people cosplaying as her long before she officially appeared in a comic!. And less than a month after she finally appeared in a comic, she gets his personal ongoing series and became officially part of the Spider family.
It seems that "Gwen Stacy in alternate roles" have taken off to the point where there's going to be a Christmas-based one-shot featuring "Gwenpool", a Gwen Stacy who became Deadpool (though, thankfully, she doesn't look like she's suffering from the cancer-ridden Healing Factor normal Deadpool has), who appeared in a set of variant covers with Gwen in various roles. After her debut in Howard the Duck she gets her series, The Unbelievable Gwenpool, but she is reinterpretated as a Meta Girl (a girl from another universe where all the heroes and villains of this universe are comic book characters) with no relation to Gwen Stacy beyond their first name and hair color.
There are a number of people enamored with his "Bombastic Bag Man" getup.
People really seem to love Ultimate Jessica Drew, Peter's Opposite-Sex Clone. She's appeared relatively only a few times in the Ultimate Marvel Universe. Yet fans tend to go "oh no!" whenever something bad happens to her or squeal whenever something good happens to her.
The Punisher. Originally he was supposed to appear only in one issue of The Amazing Spider-Man. Fans liked him, so he reappeared. And then he became an enemy of Daredevil, because of their different views. He also featured in Captain America comics and some others. And when in the 80s the world was ready for a cold blooded killer to become the main character of a series, he got his first own comic book. And he was all over the Marvel Universe, not teaming up or fighting against maybe only guys really out of his league like Silver Surfer.
Moonstone was just another villain until Thunderbolts reinvented her as a Magnificent BastardJerkass. Then she had her own comic, was a part of the Dark Avengers team and sat at the right hand of Norman Osborn. Same with Songbird (helps that her hair tastes like strawberries).
Wolverine has turned into this in just about all of his incarnations. In fact, he's so popular, he's often used as a marketing ploy for other series in which he doesn't appear at all. Ironically, one of the early plans was for Colossus to be the Breakout Character and Wolverine nearly killed off in his third issue with the team (and second as X-man), which more recent fans would no doubt find hard to believe. Instead they killed his teammate Thunderbird, who had a very similar personality, largely because his powers were more generic than Wolverine's (neither a Healing Factor nor claws were particularly common powers in comic books at the time; it's largely Wolverine's later hyper-popularity that changed that).
Old Man Logan has joined the ranks, thanks to Secret Wars (2015). He was already fairly popular due to his story of being in a Bad Future where the supervillains (and a few surviving heroes) rule America, but that got expanded with Wars where he went on a journey across Battleworld in search of how an Ultron head landed in his yard. He migrates into the normal Marvel Universe following Wars, replacing the original Wolverine, who died prior to the storyline.
Several of the background characters at the Xavier Institute developed fanbases despite having no or few lines, thanks to neat visuals or powers. Notable amongst these are Pixie, a girl with fairy wings and the ability to disperse a hallucinogenic powder (and who got a miniseries); and Anole, a lizard-like mutant with superhuman camouflage powers and a long tongue.
Both of these were introduced in New Mutants vol.2, which also has a different case - the initial cast were Wind Dancer, Prodigy, Elixir and Wallflower, who were later joined by Surge. After the book's relaunch as New X-Men: Academy X, they got a rival team in the new Hellions. Once Craig Kyle and Christopher Yost took over the series, they decided to focus on the most popular characters. Which were Surge and two thirds of the Hellions.
Under the hand of Peter David, Shatterstar has been the subject of extensive online debate, beaten up The Thing, kissed almost as many people as the rest of the cast put together, been featured prominently in at least three different covers, made himself a very likely candidate for a limited series, and just generally stolen the spotlight both in-universe and out; all this in, what, ten issues or so? Not bad for a character who the writer refused to allow anywhere near the book for quite some time.
Peter David took a bunch of nobodies, and made them into a team in the much beloved X-Factor series, specifically the one centering around X-Factor Investigations. The biggest examples would be Jamie Madrox, the Multiple Man, and Layla Miller, who went from The Scrappy of the House of M event to one of the series' most popular characters.
Kitty Pryde has managed to return into mainstream comics despite every X-Men writer not named Chris Claremont giving no crap about her. Joss Whedon made her popular again in Astonishing X-Men and Kitty even took over as leader of the X-Men which is a mighty jump from where she started.
Blink also gained quite a fan following after a fairly brief existence in their mainstream storylines, due to her unique look and interesting variation on semi-common teleportation powers. She got an upgraded role in the Age of Apocalypse storyline, which in turn upgraded her popularity. She was so popular that she survived the destruction of that universe and became a main character in the Exiles spinoff.
In many ways Cyclops is this, his troubled nature, his polarising actions for fans and creative use of Eye Beams has put him on a level somewhere just below Wolverine. Depending on the Writer Scott can be the unsung hero, infidelic asshole or radical zealot.
Storm could certainly qualify. While she wasn't a side character when she started out, they probably didn't expect her to become a hit, much less become probably the most recognizable black superhero.
Gambit is a character that has somehow endured since the 90s combining the best elements of grizzled smoking badass and dashing Swashbuckler, not mention his Badass Longcoat. Gambit even managed to make it out of the much reviled X-Men Origins: Wolverine with dignity as Taylor Kitsch portrayal of Gambit was one of the few decent things in movie. Nowadays, Gambit along with his eternal love Rogue have got a solo series making them both Breakout Character(s).
Nate Grey a.k.a. X-Man, from the Age of Apocalypse, qualifies, getting a solo series that lasted for over six years and 75 issues, being one of the key players in the Age of Apocalypse and Onslaught, the two big X-Events of the 90's, and hanging out with Spider-Man, the X-Men and even - briefly - the Avengers, before stealing the show on his return in Dark X-Men, in which he proceeded to play the entire cast like a fiddle. Pity the Green Goblin persona wasn't as self-destructive as he thought. After that, he had a solid role in the New Mutants until Marvel NOW, before returning in Uncanny X-Men (2018) with his full power-set as the Well-Intentioned ExtremistBig Bad and sparking the X-Men's Bat Family CrossoverAge of X-Man. Not bad for an alternate reality version of Cable.
Among X-Statix's frequently rotating cast, few stood out as much as the team's teleporter, U-Go Girl, a cute blue-skinned Southern Belle with a Tear Jerker of a backstory and probably the most functional moral compass among the Unscrupulous Hero team. Writer Peter Milligan was well aware of her popularity and chose to herald a major turning point in the story by killing her off - years later, reflecting on the series, he considered doing that his biggest mistake.
Kate Bishop (Hawkeye). She's the only character without some sort of legacy attached to the Avengers themselves, and took the name of a character that was unceremoniously killed off, so you think she'd be hated. But no, she is by far the most popular member of the team, to the point where, even after Clint came back, she got to keep the Hawkeye name. She was so popular that she even became deuteragonist of Matt Fraction's Hawkeye ongoing, where her popularity increased even further.
Miss America Chavez. Despite her rather minor role, her new Civvie Spandex outfit became popular with cosplayers before the series even started and towards the end of the series even Kieron Gillen admitted that from fandom output and the way she somehow worked her way into the center of later covers, he feels like she is the character his run will be remembered for the most.
Broo, a mutant member of the Brood Alien race that causes problems for the X-Men. After a small appearance, he vanished until Wolverine and the X-Mencame onto the comic book scene, where he ended up being one of the series' most popular characters, and one of their most popular students. Kid Gladiator, another alien, also gets a lot of love.
The success of the Deadpool movie has not only made interest in the character explode, but Domino's as well; fans are practically begging for her to be in a possible sequel. Just go to DeviantArt and put her name into the search engine to see as many hits recently as the X-Ladies.
Many of the characters who came to be reintroduced in mid-90s revival series also experienced this sort of status. Chief among them Animal Man and the Doom Patrol (both reimagined by Grant Morrison), The Sandman (to the point where most people outside of comics don't even realize how deeply ingrained DC continuity is in this character's history), Kid Eternity and of course Starman.
Dick Grayson (Robin I/ Nightwing I/ Batman III) is so popular he's this for the whole universe, to the point that Geoff Johns refused to kill him off as instructed on the basis that he was The Heart of the DCU and his fanbase was too damn big. His Nightwing series was a consistent strong seller and was only cancelled because he was becoming Batman. As Batman, he completely averted the Replacement Scrappy trope and ended up having more ongoing series than Bruce had once he came back.
Tim Drake, due to being far more relatable than most Bat-characters, is also an example of this, even among Robins. Before him, the Robin mantle in general was widely derided for being a campy Silver Age throwback, with Dick firmly in the role of Nightwing and Jason being killed off. However, he managed to make Robin work by being competent enough to not need Batman holding his hand or coming to his rescue, working hard to earn his rank, and being a nerdy teen and thus able to identify with. Unlike Dick, who is generally considered to have been Rescued from the Scrappy Heap once he became Nightwing and Jason, who did the same (kind of) once he became the Red Hood, Tim is considered to have been great from the outset. His popularity also led to him being the first Robin to get an ongoing series.
Damian Wayne, Batman's son, was initially intended to die after his first storyline, and was widely disliked by fans for his bad attitude and violent behavior. He was then made into the new Robin, and became the co-headliner of the immensely popular Batman and Robin series, where he developed a brotherly friendship with Dick Grayson that people absolutely adore. Peter J. Tomasi would then further rescue Damian in the second Batman and Robin series, also immensely popular, where he worked with his dad. He has since developed a sizable fanbase, even being briefly added to the Teen Titans as part of a stunt to raise the title's sagging sales. This still didn't stop his creator from going through with his original plans and finally killing him, but he got better in a timely fashion and would get another ongoing once Batman and Robin ended, and then appear in Superman and get another series with Jon Kent with Super Sons.
Another, earlier example is Stephanie Brown, the fourth Robin and third Batgirl, respectively, and was an Ensemble Dark Horse in the Robin book before War Games killed her off. After her death, however, her popularity with the readers caused not only for her death to be retconned - but also for her to be made the newest Batgirl with her own (Batman Beyond-esque) series with Barbara Gordon. Unfortunately it was cancelled, and Stephanie got sent to Comicbook Limbo before being revealed to have been retconned out of existence entirely, not re-surfacing until 2014 as the Spoiler. It's become clear that Stephanie is an invertedCreator's Pet — she has a vocal fanbase, but the higher-upsdo not like the character. (Expect Popularity Polynomial to reverse this one day.)
Similarly we have the second Batgirl, Cassandra Cain. Despite her origins as a Replacement Scrappy for Barbara Gordon, she had her own series and built up a sizable fanbase, and there was an extreme backlash to misuse of the character. Like Steph, she was retconned out of existence to make way for Barbara's return, but there was a noticeable air of resentment from many fans, and she was eventually brought back in 2015, albeit with an altered backstory and not as Batgirl (which is still a point of contention). Like Steph, it's become clear that Cass is a character the fanbase adores, but that the writers hate.
A lot of GCPD officers and detectives such as Renee Montoya, Harvey Bullock, Crispin Allen, and Jason Bard are extremely popular, sometimes even being considered part of the Batfamily.
A bunch of the more obscure Batman Inc./Club of Heroes members are really popular with fans such as Batwing, El Gaucho, Nightrunner, and Batcow.
Black Mask is frequently cited as an example of a great Batman villain who is woefully underused. Maybe it's his cool look or maybe it's his Xanatos-style intelligence, but in any case fans seem to really like the guy. Him getting Hijacked by Ganon in Arkham Origins just caused much of the fanbase to clamor even harder for him to get a day in the limelight.
Technically, Batman Beyond star Terry McGinnis is this. Like Harley Quinn and Renee Montoya he was taken from the DCAU due to his massive popularity and moved into the main universe as a possible alternate Batman — though whether or not he's still Bruce' son (and Damian's younger brother) in that future is uncertain. His popularity created several comic series, and he was even brought into the main DCU again in the New 52.
Killer Croc is very well-loved when he's written as a Noble Demon. In the New 52, he got a big popularity boost after his sympathetic portrayals in Batman Eternal and Gotham Academy, which paint him as someone who just wants to protect those he cares about.
Batwoman, the first high profile lesbian superhero, got this from the outset when she appeared in 52. She eventually got her own ongoing as well as a supporting role in Batman, Incorporated.
Jaime Reyes, the Blue Beetle, having an immensely fan loved series Pre New 52 and post New 52 still retaining this, lasting a while despite low sales due to strong fan love. Pretty impressive given that as an Affirmative Action Legacy character whose predecessor Ted Kord had been killed off for Countdown to Infinite Crisis, he ran the strong risk of ending up as a Replacement Scrappy.
The New 52 revival of Dial H saw two major popular characters. First was Boy Chimney, the first hero Nelson dialed in the first issue, an eccentric, lanky figure with a hide as tough as bricks and the ability to create and manipulate smoke. He would later be joined by Open Window Man, a superhero in his own right and one of the only members of the Dial Bunch to get any significant panel time (including an entire issue devoted to him). And that was at the point where the series was being cancelled. Two things helped Open Window Man: 1) he was the crime fighting partner of Boy Chimney back when he was alive, and 2) because his origin reveals that he's basically Batman but with a window theme.
Golden Age example: The Red Tornado was originally introduced as "Ma" Hunkel, a supporting character in "Scribbly the Boy Cartoonist," but was so outrageously silly that she completely overshadowed the title character. 60 years later, Ma was the curator of the Justice Society of America museum, and nobody remembers poor ol' Scribbly.
Wildcat. A lot of modern fans don't realize that in the 40s, Wildcat was just barely a member of the JSA, participating in exactly two JSA stories of the time. He became more popular during the 70s JSA revival and All-Star Squadron, and then really took off in the modern series. It helps that he's one of the few remaining living team members.
This is similarly true of many JSA members of that era. Hourman, Dr. Mid-Nite and others were completely failed concepts that would likely have vanished forever if not for their JSA links - which allowed future writers to bring them back in future storylines. Both had further runs, and currently popular successors.
Within The Flash comics, the older speedsters tend to get a lot of love:
The original Golden Age Flash, Jay Garrick. The guy doesn't develop much in his modern appearances, and he's largely a supporting character even within the beloved JSA series. But you'll find nobody, from Flash fan to wider DC fan, who doesn't just love the old man. He's theCool Old Guy in the DCU, and a father figure to several generations of heroes. He's also one of the nicest guys alive, and even fellow heroes love the guy.
Similarly, Max Mercury, another Golden Age speedster. He was introduced into the DCU with a case of Remember the New Guy?, but his sage wisdom and zen attitude; interesting backstory and touching father-son relationship with his polar opposite Bart Allen, endeared him to readers. He's also sorta responsible for bringing the Speed Force into the franchise.
In the 80s, it was Kilowog, who's still a fun character and a foil to the four Earth Lanterns. Recently, it's Mogo the living planet, who was introduced in the 80s and then rarely used until Green Lantern: Rebirth. He's had a lot to do since then, including being a key being in Infinite Crisis and the Sinestro Corps War storylines.
And of the four Earth Lanterns, Guy Gardner is himself the darkhorse; originally a one-shot character who was brought back just so that he could be injured and John Stewart could take his place, writers just kept using him. He eventually became a sort of tragic-comicAnti-Hero, and his popularity and thus notability increased dramatically. He even got his own solo series for a while in the 90s and another in 2010.
Ganthet. The only non-Lawful Stupid Guardian on all of Oa. Had the Fridge Brilliance moment of realizing that when a Lantern's hopeful, their will exponentially increases. Hence why he's the man.
Arkillo has fast become one as well thanks in no small part to the massive amount of character development he received.
Alan Scott is strikingly popular, despite having essentially nothing to do with the modern mythos and often not even existing in the same universe. Every comic he shows up in gets wide praise, and he seems to have little to no hatedom relative to the other human Lanterns.
Jonah Hex of All Star Western. His book was one of the highest rated books, and the lowest selling, of the New 52.
Legion of Super-Heroes started out as a one shot appearance in Superboy. They caught on and eventually edged him out of his own comic. The Legion itself is not lacking in Darkhorses; in fact it's hard to find a character that doesn't have a solid fanbase, Chemical King and the Legion of Substitute Heroes most notably. The biggest example of an ensemble darkhorse for the Legion of Super-Heroes is Wildfire; originally a one-shot character who dies in his first appearance, fan response to the character led to the writers bringing him back and make him team leader, after the fan-voted leadership election for the year he joined the team had him win. Though he's largely been absent from the book since the 1989 "Volume Four" reboot, he has a vocal fanbase that has kept the character at the forefront of the property. Like that other facelessEnsemble Dark Horse, part of Wildfire's appeal is his unique design.
The Night of the Owls storyline introduced several Talons, assassins of the Court of Owls who attacked many members of the Bat Family. Most haven't been seen since and are in cold storage, but the one who attacked Batgirl, a victim of Japanese air balloon bombing in World War II, returned for the Batgirl Annual and has joined the Birds of Prey as Strix.
In the '80s Will Payton version of Starman, his sister Jayne and mother Jo Marie were more popular with fans than Starman himself or any of the villains.
Static maintains a lot of fans, despite his comic being one of the first New 52 titles to be removed and his long absence from television. In Young Justice, he is one of the most hailed characters in the trailers. Strong fan love for fellow Milestone Comics characters Rocket, Icon, Xombi and Hardware is also this.
Supergirl started out as a test to gauge fan interest in a female character with Kryptonian powers. Fan reaction was incredibly positive, and DC introduced a proper Supergirl -Kara Zor-El- the next year. Six decades and hundreds of comics later, Supergirl is still one of the most popular characters of the Superman mythos, even though DC killed her and tried to get the fandom to forget about her in 1985. They failed and evventually had to reintroduce the character.
Her Earth-2 counterpart Power Girl also qualifies due to being one of the most well-knownsex symbols in DC Comics (there is a good reason she is the trope image for the comic book sub-page), even though she is not considered a A-list superhero nor really focused or used much, but she still has her very devoted fanbase regardless.
Bizarro. Only appears every once in a while and rarely plays a major role in the story, but beloved for his goofy and lovable personality, plus his at-times legitimately tragic nature. Notably, he died in his very first appearance, decades ago, but fan outcry resulted in him being reborn via Applied Phlebotinum soon afterward.
Mr. Mxyzptlk, mainly for always being really funny whenever he shows up.
Krypto the Superdog. Cheesy maybe, but the dog is so brave, loyal, and just plain fun that he'll always be a welcome part of the Superfamily.
Jon Kent, the third Superboy and Clark and Lois' son. Right from his creation he was adored for finally allowing Superman and Lois Lane to have a child, something fans have wanted for decades. Also, given the Younger and Hipper bent DC was on at the time, him allowing Superman to be a father was seen as a welcome change. Speaking of that, with Jon's introduction, writers were finally able to write newer types of stories for Superman, where he struggles with parenting, a problem he can't punch away. Jon himself is also beloved as a return to typical sidekick roots after years of deconstructing the concept, as he's a Nice Guy like his father with his mother's curiosity, with a well-written relationship with his parents and angst about living up to his father's legacy. He ended up co-starring with his father in Superman (Rebirth), where he sometimes gets more focus than the titular character, and very quickly got an ongoing alongside Damian Wayne, Super Sons.
Terra from Teen Titans. She lasted little more then a year in the comic, but is one of the most well-recalled characters in the series. A "different version" of her (who might or might not have been the original with amnesia) was brought in a few years later only to eventually be killed off and replaced by a THIRD one, who became the best friend/sidekick to Power Girl, then went on to befriend Starfire.
While the short-lived comic The New Guardians has been largely forgotten, Linkara'sreview of the second issue gave special attention to one character: Snowflame, a Crazy Awesome one-shot villain who derives superhuman strength from snorting massive amounts of cocaine, which he verbosely revels in and hails as his god. Two crack-addled rants and a beatdown later, he becomes Linkara's favorite character, and now commands a significantly larger fanbase than any of the heroes.
And although he only made one comic appearance he lives on through frequent appearances in Atop The Fourth Wall and his own Webcomic.
The Legend of Wonder Woman (2016) version of Etta Candy has become very popular and arguably the most well-known aspect of the already well-received miniseries. It helps that unlike most versions after the Golden Age, she is neither slim nor does she feel particularly insecure about her weight, being simply a modern take on her original Big FunAction Girl version.
Speaking of Wonder Woman, there is Artemis of the Bana-Mighdall. Introduced as an Anti-Hero Substitute of Diana in the '90s, Artemis was killed off but resurrected due to her popularity as a Foil to Diana. She has since become the most focused and developed of not just the Bana-Mighdall tribe but of the Amazons as a whole and is considered one of the most iconic Wonder Woman characters.
Death from The Sandman. She was originally meant to be a minor recurring character who might appear a handful of times, but her instant popularity with the audience — helped no doubt by her perky, upbeat, kindhearted nature, a sharp contrast to most personifications of Death — was so strong that Gaiman made sure she'd get at least one appearance in all ten volumes. These appearances vary in size but always feel substantial, and their sparsity helps prevent the story from ever focusing on her too much. Not to mention she's become canon in the actual DC universe.
Watchmen has a flock of these in the form of the Minutemen. Also a good deal of the villains that are mentioned offhandedly, most notably the Twilight Lady. Perhaps more notably, Rorschach is much, much more popular than Alan Moore intended.
Raul the Cat, from American Flagg!. He even won the Comics Buyer's Guide Fan Award for "Favorite Supporting Character" in 1984.
A later comic had Sabrina switch everyone's gender. Fans really want more of Reggie's counterpart, Regina, who is a proper Alpha Bitch.
Archina and especially J.J. are very popular (a picture of them and Regina can be found here◊). Archina has cute Girlish Pigtails and people enjoy her reverse harem more than the usual version, while J.J.'s fashion choices, apathetic personality, and Big Eater qualities make her attractive to people (much more so than normal Jughead).
NICOLE. Originally just a handheld computer of Princess Sally's hailing from the future, she was nothing more than a prop from the old days of Sonic the Hedgehog's Saturday Morning cartoon. Then, a story came out where an accident allowed NICOLE to experience life in Sally's body. Drawing from that, she constructs a Hard Light lynx form for herself, sharing it with Sally privately. A few issues later, she aids Sonic and Shadow, showing her form to the others. Come the post-Sonic the Hedgehog/Mega Man: Worlds Collide storyline, she's now one of the Freedom Fighters and a massively popular character in her own right.
There's also Scourge the Hedgehog and, by extension, the Suppression Squad. When they first appeared, Scourge was just "Anti-Sonic", the Suppression Squad the "Anti-Freedom Fighters" and their homeworld of "Moebius" was just "Anti-Mobius". Even their looks were bland - they were just "Freedom Fighters in leather". Anti-Sonic was so ineffectual, his lowest point was being dropped by Antoinecompletely by accident. Under the pen of Ian Flynn, however, he shed all of those traits, getting a new look and taking a breaking speech to heart, becoming a massive threat.
Battle Chasers: Red Monika. Even though the comic might be obscure these days, she is the main reason why anyone still remembers it due to the amount of pin-ups and fan art spawned by it, which is ironic, considering she was a secondary character to Garrison and Gully, who were the story's point-of-view characters.
G.I. Joe's Snake-Eyes. The character created only so that the company could sell another figure without having to pay to paint it ended up becoming the posterboy for the franchise as a whole.
Patty (and by extension, her gaming group, Patty's Perps) is very popular with the fans. It seems that almost every issue includes at least one request from fans for "More Patty!"
Crutch (who is, incidentally, a member of Patty's group) has amassed a respectable fanbase of his own. Readers responded well to the sympathetic portrayal of his criminal past, and his determination to keep his nose clean. The awesome Crime Nation the RPG campaign he started running helped matters.
Gordo has his fans, mostly for his unshakable niceness, even in the face of Stevil's constant bullying. And he has one kickass home gaming setup, complete with special lighting, aromatherapy machines, and a sno-cone maker.
Bug from the Micronauts was originally just the Plucky Comic Relief on the team but as time went on, he became a more sympathetic three dimensional character. Along with his own one shot comic, he also got to appear in non-Micronaut titles such as Guardians of the Galaxy and according to Word of God, he came very close to being in the movie.
He's the most despicable character; a real shitbag. He enjoys torture, and readers can't get enough," said Azzarello. "In one of Lono's earliest appearances, he had a woman tied to a bed and raping her! I figured that should solidify him as 'the bad guy'. But I guess not.
Scrooge McDuck was originally intended to be a one shot character in Carl Barks's comic Christmas on Bear Mountain. But due to the unexpected popularity of the character he became a recurring character in the Donald Duck comics, eventually getting his own comic book series, and eventually making animated appearances.
In Wildguard "Freezerburn" was originally going to die in #4, but the series site poll showed him to be one of the most popular characters. Crag Langley was dispatched instead. Freezerburn ultimately won the poll, out of a very big field of applicants, to become a member of the final team.