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).
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 different case - the initial cast were Wind Dancer, Prodigy, Elixir and Wallflower, who were later joined by Surge. After book's relaunch as New X-Men: Academy X, they got rival team in 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 fo the series' most popular characters.
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.
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.
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. Not bad for an alternate reality version of Cable.
With the exception of Jason Todd (though ever since he became the Red Hood, even he's gotten a fanbase now), each of the Robins tend to have a very devoted fanbase just to them. Dick Grayson is so popular he's this for the whole universe, to the point Geoff Johns refused to kill him off as instructed on he basis that he was The Heart of the DCU and his fanbase was too damn big.
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.
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. He has since developed a sizable fanbase, and Batman and Robin continues to be a strong seller. He was even 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 killed him.
Another, earlier example is Stephanie Brown, the fourth Robin and Batgirl respectfully, and was an Ensemble Darkhorse 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, not re-surfacing until years later 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 third Batgirl, Cassandra Cain. Despite her origins as a Replacement Scrappy, she had her own series and built up a sizable fanbase. Since the New52 she hasn't been seen at all.
Technically, Batman Beyond star Terry McGinnis aka Batman II is this in The DCU. 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 (presumably after Dick Grayson's and Damian Wayne's Batmen retire) - though whether or not he's still Bruce' son (and Damian's younger brother) in that future is uncertain (Waller's motivation would need adjusting). His popularity created several comic series, including the current ongoing series (and his show even got its own Spin-Off, The Zeta Project).
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 is 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.
This has happened to a few members of the Green Lantern Corps. 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.
Hell, the Red Lantern Corps as a whole. They're getting their own series.
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.
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 Darkhorse, part of Wildfire's appeal is his unique design.
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.
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.
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.
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.
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 starberries).
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.
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.
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 an Internet Backdraft much stronger than the death of Wasp, founding Avenger.
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.
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. She has a long debate about mortality with Lex Luthor in Action Comics #894 (part of the "Black Ring" story arc).
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.
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.
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.
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.
Terra from Teen Titans. She's ashated as she is loved. 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 has become the best friend/sidekick to Power Girl.
Raul the Cat, from American Flagg. He even won the Comics Buyer's Guide Fan Award for "Favorite Supporting Character" in 1984.
Out of DC's big three Wonder Woman certainly is the Ensemble Darkhorse. She's been unable to get the love and appreciation that either Superman or Batman have, no thanks to never having a Live-Action Adaptation (aside from the 70s show) or a cartoon series; she also rarely pops up in cartoons to the point where Green Lantern has begun to replace her as a part of the "Big Three". Few outside of the DC fanbase know much about her other than she's an Amazon made of clay who has a lasso.
She's made of clay?
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 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 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 Internet Backdraft 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.
Kate Bishop (Hawkeye) of the Young Avengers. 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 popular increased even further.
Another example from Young Avengers is Miss America Chavez. Despite 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 admited that from fandom output and the way she somehow worked her way into center of later covers, he feels like she is the character his run will be remembered for the most.
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.
Speaking of New 52, Jonah Hex of All Star Western. His book is one of the highest rated books, and the lowest selling, of the New 52.
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.
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 was killed off specifically to make room for him, he ran the strong risk of ending up as a Replacement Scrappy.
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.
Batwoman, the first high profile Lesbian superhero.
Obidiah 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.
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.
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.
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 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.