Midoribom AKA Racer from Bomberman Land Parody is quite popular despite only appearing in that one comic in the entire Bomberman fandom. He is featured the most though
Roast Beef, Ray and (to a lesser extent) Pat from Achewood were originally part of "The Dirtiest Guys in Town," a group of nondescript cats who hung out together in early arcs. Ray and Roast Beef later became the main characters of the strip and Pat a notable supporting character.
Fail-Druid and Rob from Ctrl+Alt+Del, despite the fact that they're supposed to be annoying, are the most beloved characters in the series.
Sasha. Riff's girlfriend for under two years out of the strip's 10+ year run, enjoyed lasting popularity despite not making any in-continuity appearances between mid-2002 and mid-2009.
There was also Bert, Torg's artist friend with a disturbing obsession with crotches. He proved to be so popular, his life was spared in the KITTEN arc, which was written with the full intent of killing off a bunch of secondary characters. He was eventually killed off in the KITTEN II sequel arc, but still lasted much longer than originally intended, and even returned for a while as a ghost.
Crushestro, one of the villains introduced in the "Paradise" arc, gained significant popularity due to his over-the-top mannerisms. He made a reappearance for another Breather Episode. He then later ended up teaming up with Torg to fight Bestseid.
Originally, Nale was supposed to be the only member of the Linear Guild who survived their encounter with the Order. But fans latched on to the Psychopathic Man Child Thog, so Rich Burlew made him (and Nale's girlfriend Sabine) recurring villains.
Cassie SinClair seems to have a much bigger following than main character Anne Onymous, despite her appearances in canon being rather sporadic.
This is probably due to shipping: Robin/Cassie is much more popular than Robin/Anne. Also, her sporadic appearances seem to help her avoid the Idiot Ball.
In a less typical example, despite the main comic making Jason's receiving of a Gender Bender as a major running gag it seems to be more popular in fan work to apply it to Robin instead.
Robin makes the cuter girl. Or maybe it's just because Jason's transformations were being overdone at this point.
Zexion from Ansem Retort is a prime example of this trope. Originally planned to be the straight man to Axel, he gradually became more of the jerkass, and his popularity grew with it. By Season 2, his gradual descent into being a jackass had become a free fall. His popularity grew to the point that Season 3 focused entirely on him, he's featured in the intro image to the website, and is arguably the most popular character in the entire series.
A Darkhorse Race would be the Jägers in Girl Genius. Originally amusing background characters, they were so popular that they became a major plot element, and 4 joined the main cast. More specifically, Da Boyz, a trio of Jägermonsters sent to find a remaining Heterodynes (plus Jenka). Also the Girl Genius Wiki has a suprising amount of support for the nyar spider, a small spider that appears in one comic, wraps up a bad guy for dinner, and is promptly squished. People were oddly happy when it turned out this was a species, not an individual.
Steve really only exists to give Marten a male friend, but he has a loyal following that wonder what he's up to during his long absences from the comic. When the answers are like this, it's no wonder.
The fourth-wall breaking filler character "Sweet-Tits" became an instant favourite, despite only appearing twice and never being coloured or given a proper name.
According to the results of a "most popular character" poll, the most popular character (by far, scoring twice as many votes as the runner up) is... ...Hannelore! It surprised the hell out of the author.
Kamikaze Kate from Misfile has managed to be far more popular than her number of appearances would seem to warrant.
Ozy and Millie has had a handful of one-shot, or even one-panel, characters who gained a fandom. They include Edwin the clueless juror, Emily the schoolgirl skunk, and Stevie the black cat. The latter two have reappeared on occasions when the cartoonist needed extra students, but they remain Flat.
Doctor Hot from Checkerboard Nightmare. The author rolled with it and expanded his role, to further fan approval, but that didn't mean he had to like it. As his cast page describes him:
Hacky, sensationalist TV pop psychologist who appeared in ONE LOUSY PANEL whose single-word catch phrase has been adopted by "Checkerboard Nightmare" fans.
We have the Allosaurus. He first appeared infrequently, but after fans grew very attached to him he started being more commonly featured, his growing popularity eventually led to a successful presidential campaign. He also has the distinction on of being one of the few characters that invariably prompts mass-hacking into the popularity polls.
We have Caylin Bren, evil blonde leader of The Chosen. Caylin's head got exploded by Luna, but there's just enough evidence suggesting he could have lived through it that it didn't quiet his fans. He was also written into the maligned Snowsong story arc, appearing in several flashback strips. Bren's popularity appears to have waned over time.
Katherine from Wapsi Square, a fairly minor supporting character, developed a fanbase rivaling most others, prior to the major shift in subject and tone. Fan demand led to her being one of the few supporting characters who were carried over after the change; although her role remains minor.
Bard from 8-bit Theater was only seen in a one-panel gag as the "fifth Light Warrior" who was unmade by Sarda before his birth. He is quite commonly mentioned in the comic's forum, with some members even managing to trick a few people that he actually was in the comic at first and the creator retroactively replaced earlier strips with Bard-free strips - a tactic the author actually pulled off on a smaller scale before.
Kingsonnn Dededoo from Brawl in the Family initially appeared in one of the gag-a-day strips, but became a fan favorite on the forums. He has since made at least one more appearence.
Despite being The Scrappy in the video games, Waluigi is - WALUIGI TIME. Waluigi is funniest character in the comic. Waluigi makes everything better, and - GACK! Ahem. Waluigi is an even bigger Darkhorse, as he debuted in a series of Dada comics Matthew made for April Fools' Day. In fact, Waluigi's become so popular thanks to Bit F, his canon counterpart's gone from Scrappy to Base Breaker status.
Dr. Lee, from Skin Horse by Shaenon Garrity and Jeffrey Channing. She was in one series, as the MeganekkorepressedMad Scientist and one of the antagonists, but she is still being requested by fans, and drawn in fan art,
The best example would probably be Ms. Paint, a random background character in Prospit that became well-known due to her Punny Name and unique appearance, but has absolutely no bearing on the plot whatsoever.
Another good example would be Fedorafreak, a character who has "appeared" in the form of background messages on John's dad's PDA a grand total of maybe four times. There are people who roleplay as him.
All of the post-scratch trolls in the series seem to be radically more popular among the fandom, judging by the staggering amount of fan art, fan fiction, and cosplaying there are of them as opposed to the actual main characters.
Nepeta is another good example. Despite being very popular among the fandom, and appearing in a ton of fanart, she's probably the least important of the trolls. All she's done that's of any significance is being Aradia's server player, having someone to fill the "Leo" slot of the troll's zodiac motif, and asking Rose to talk to Jaspersprite. The latter of those three leads to Rose leaving Jaspersprite seemingly for good, but that's still a relatively minor event.
These troll's ancestors are also pretty popular, considering how eleven of them only had the sum total of two comparatively small arcs covering them, and a very quick recap given later into Act 6. The twelfth? In a possible nod to this, she's the biggest villain in Act 6 bar Lord English himself. These people probably have more fan works devoted to them than the guardians of the main characters, who are, putting it simply, the human equivillent in their role of the Geodesic Cast. Heck, on the wiki, their page is the second top right behind the one on trolls in general.
Jake English became one very quickly, and his popularity borders on Memetic Badass / Memetic Sex God at times. It probably helped that his debut finally gave some resolution to who the hell Jade's penpal was anyway. Although he would later go on to become something of a small Base Breaker after he gets into the game.
The main character of Post scratch Rose's book series, Calmasis, has to be the worst offender of this in the history of the webcomic. Possibly no more significant than a passing mention and possible foreshadowing of other events, s/he has hundreds of pieces of fanart and has already spawned several fan theories hours after their debut update. Yes, a character within a book within a webcomic who was only described in detail on one page has quickly risen to massive popularity, already rivaling several other main characters who were given thousands of pages to flesh out. Only this fandom could do this.
Much like Calmasis, an unknown dead troll suddenly garnered tons of fanart before speaking even a single line. Granted, Aranea has since interacted with a good portion of the main cast, and she was directly involved in setting up the events that led to the troll's session.
The Felt. Despite being a Quirky Miniboss Squad made specifically for the Midnight Crew Intermission, they became very popular among the fanbase. So popular that they may have increased their importance among the comic; Act 5 introduces Doc Scratch, a new member of the Felt, and reveals that Felt boss Lord English is a time-traveling demon with a connection to the Troll Universe. It turns out Scratch and English masterminded the entire plot of Homestuck. Speaking of the Midnight Crew...
Problem Sleuth: the Midnight Crew debuted and appear exclusively in several donation commands, "[waging] merciless, donation-funded warfare against the protagonists in a non-canonical but nonetheless grand plotline.". They later became a fundamental part of the plot of Homestuck, both as themselves and as alternate universe counterparts. Such was their popularity that Hussie briefly gave serious consideration to doing a Midnight Crew adventure instead of Homestuck.
Not only do they appear, but their alternate reality selves play a big part in the comic. This also sets forth a very confusing game within a game scenario.
Lolrus from What Do You Do is incredibly popular for something that only appears like 7 times out of over 700 panels.
Erfworld has several, some of which the authors delight in putting in, even as background characters. Most notable is "Scarlett", the unnamed redheaded Unaroyal warlord who has since her first few appearances been decrypted and joined Gobwin Knob and continued to appear frequently. Also, Vurp, the last surviving Hobgobwin after Chapter One, and to a lesser extent Sizemore, the most underused Caster.
Now that Scarlett's been given a name (Sylvia), she may count as an Ascended Extra by virtue of this trope.
Ples Tibenoch of Hanna Is Not a Boy's Name already had a massive fanbase before he was even introduced into the comic, all based on a few doodles and lone illustrations from the author.
Don't forget the unnamed cashier from the liquor store! He appears in maybe 3 pages of the whole story, yet fans have latched onto him, affectionately dubbed him "CA$H MONEY", and you should just see how much fanart he has.
The best example would probably be Leonest. He was the first black marketeer the protagonists had to deal with, a demon-obsessed drug dealer. Thanks to his cool design and deadpan attitude, he became instantly popular, and was upgraded to secondary cast member (Though all he did was hang out with the protagonists at their office between missions/during the Beach Episode. It's implied that he started doing other work for SinTech that doesn't overlap with what the protagonists are doing).
A rather odd example would be Matthew. While ostensibly a member of the main cast, he barely got any screen time — only a small side plot about him stalking his brother's girlfriend that eventually got co-opted by Joey anyway. Didn't stop Matthew from being more or less the strip's most popular character. [[spoiler: However, Matthew recently gained a lot more importance due to him becoming The Mole for Vlad. Amusingly enough, the reason for his betrayal was that he was never given anything to do — in other words, because he didn't get enough screen time.
Zig Zag, the titular character's porn star boss in Sabrina Online, has gradually been taking over the strip, to the point that the December 2010 group of strips focuses on Zig Zag and doesn't feature Sabrina at all.
El Goonish Shive has Chika who won this status after five Q&Acomics with her, even despite general "enough of Q&A" reaction on EGS forum.
Before either of them was Susan, who was originally intended by the author to be a minor secondary character and has long since become a firmly established member of the main cast with multiple tragic backstories and some of the most visible character development of any of them.
Looking for Group has Richard, who is without a doubt the most popular character in the whole story.
Alexander Hamilton is not, by any means, a major character in The Dreamer. He showed up in the middle of Issue 9, played a small role, and was gone by the end of Issue 10. You would not know this from looking at his fanbase. Oh, the shipping!
Freakangels features 12 of the eponymous psychics, about eight of whom function as major characters. The spaciest and strangest of the lot, Arkady, is the most popular character with the fans. (Of course, she's also the only one who is perpetually sweet-tempered — the rest of the Freakangels range from deeply cynical to downright murderous.)
Cookie Monster from Gunnerkrigg Court has appeared in two comics and one Bonus page so far, but almost all of the comments on those pages are about her. Turns out, one of her roles was transition to the whole chapter in the Foley House (her style obviously is — and was confirmed to be — influenced by Foley kids).
Tempest of Domain Tnemrot gained a large following on her first page and when the story's focus switched to the main characters, there were complaints she didn't get more screen time.
Penny Arcade has Tycho's niece Anne, also known as Annarchy. While almost all cameo characters in Penny Arcade gain massive fan followings overnight, Anne deserves special mention, since when a poll was held to determine which minor character should get their own guest strip over Comic Con, Anne won by a huge margin.
Digger has Ed, who started off as just a random hyena-monster the author created because she couldn't draw a bear, and ended up being a Woobie and probably the most beloved character in the entire comic.
Tiffany from Precocious has this spot decidedly locked down.
Although Yvette, the shy grey cat who appears every now and then is also becoming popular.
The curtains, every time fanmail appears, there is always one on the end dedicated to the curtains. Unfortunately, Suede didn't take then with him after he moved (they were his parents', but still...).
Nella! It really says something that all videos she's in get dozens of comments about on how awesome she is and how she should have her own show. And the Chick seems to be listening - Nella now shows up in almost every episode.
Linkara. One of many contributors who joined the site in late 2008, and plucked from almost complete obscurity, he quickly rose to become one of the site's biggest draws in only a few short months. Part of this was his unique niche (he is one of two Comic Book reviewers on the site), part of it was his consistent schedule (and at first, he posted more than one video a week, because he had a backlog of video reviews from before he joined the site), and part of it was his Colbert Bump from Spoony, who became a frequent collaborator. As early as January/February 2009, there was talk of him headlining a "comics and animation" section of the site called "Four Color Fantasy" (later renamed "Inked Reality"), but in fact he's so popular he's still listed separately, as an individual, on the site, a distinction shared only by Doug, Lindsay, Brad and Noah.
takahata101 of Team Four Star ended up getting a lot of attention thanks in part to his portrayal of Nappa. LittleKuriboh would even lampshade his popularity by mentioning one of the best way to have a abridged series is having takahata provide a voice in the show.
Nappa from Dragon Ball Z Abridged has easily become one of the series most popular characters, to the point where he had been making occasional appearances as a ghost despite having been completely forgotten in the original work after his death. The Abridged version of the Abridged series lampshades this by giving Nappa the line "I am hilarious and you will quote everything I say!"
Dad from Awesome Video Games is very big with the show's fandom, to the point where they requested he get an episode all to himself. He eventually did get one with a larger focus on him, where he transformed the show into "Computer Entertainment Related Programming" to review Jack Nicklaus' Greatest 18 Holes of Major Championship Golf (misspelled as Jack Nicholson Golf in the episode title and the episode itself) on the NES.
Similarly, Deacon (Dad's actor) from Video Games Awesome! has become inordinately popular for a guy who sits in the background and says relatively little, probably thanks in part to some residual Dad-ness.
Obscurus Lupa often does impressions of characters from the films she reviews. However, while reviewing the Subspecies movies, her Radu impression took on a life of its own, and fans fell in love with her portrayal of him as a dopey, down-on-his-luck guy who's obsessed with boobs. He now has his own Spin-Off, Radu Reviews, and has been upgraded from just being a voice to having Lupa dress up as him, complete with giant Orlock hands.
In the Homestar Runner toons, Strong Bad started out as a villain who was always doomed to lose to Homestar. Now he's debatably the most popular character, and definitely one of the most recognisable.
To a lesser extent, there's Homsar. He first appeared as a one-shot gag to make fun of a typo, and over time, has been promoted up the ranks to become part of the main cast. HR's creators have joked about avoiding giving Homsar his own cartoon since they would never need to use him again.
Same goes for Senor Cardgage.
Trogdor and Stinkoman (Strong Bad's blue-haired anime counterpart) are also very popular with the fans. They even appear together in the fifth episode of SBCG4AP!
Also Eh! Steve from the Show Within a ShowSweet Cuppin' Cakes. Strong Bad insists that the main character is Sherlock, some kind of "mix between a cow and a helicopter" who is constantly trying (and failing) to get a worm out of the ground, and that Eh! Steve is a background character who delivers his Catch Phrase once an episode. Nevertheless, Eh! Steve is vastly more popular and a much more recognizable symbol of the show.
Teen Girl Squad is another good example.
Strong Bad Lampshades this, along with The Other Darrin in the email original. After the departure of "Original Bubs," his temporary replacement "Onion Bubs" became a fan favorite.
Onion Bubs! ONION BUUUUUBS!!!
Played with in-universe in Strong Bad's commentary for an old King of Town toon. He hates every single thing about it except for the Blacksmith.
Strong Bad: Oh, now this guy had some class. The Blacksmith, that guy was a good guy. I hung out with him after the cartoon; yeah, we had some good times...
Red vs. Blue has Caboose, for whom the writers originally had no real plans other than for him to be a catalyst to annoy Church. Once he devolved into The Ditz of the group, he became very popular with the fandom however.
There is a fine literal example of this in Doctor Horrible's Sing-Along Blog: Bad Horse, who gets only a couple of songs and a brief cameo at the end. Nonetheless, he's become quite popular in the fandom.
Bad Horse, Bad Horse! He rides across the nation, the Thoroughbred of Sin!
In the LoadingReadyRun fandom, Andrew Cownden is extremely popular despite not being a member of the core Loading Ready Run crew. The reasons for this are most likely his acting ability, the infrequency with which he appears, and his awesome accent.
During Desert Bus For Hope, Roscoe the duck takes the dark horse title. It just wouldn't be the same without him.
Originally just a mention in the Whateley Universe, Aquerna has become this trope. She's one of the least powerful students at Whateley Academy, and became popular enough that one of the Canon authors is now writing Aquerna stories too.
The Irate Gamer has one in the form of the Wise Sage, even some of the fans who snark and insult the show say he's a redeeming quality, in part probably because he acts slightly better than Bores, another reason why fans probably like him is the fact the person who acts as the Sage doesn't defend Bores as much these days. Interestingly enough, the Sage doesn't appear after the Aladdin review, possibly implying that Bores is either not using him again, or the Sage was grabbing too much attention that he thinks is his.
He finally reappeared for a brief cameo in his Cool Spot review, but he didn't get any lines.
Chris has seemed to figure out his Darkhorse status and now he's shoehorning in Wise Sage appearances hoping it will make his videos "look better".
Jared Clayton of SOTF-TV is also pretty popular, considering that he isn't even a contestant, just a mentor and has had all of one line (not even onscreen!) in the actual game. This is probably due to the in-character twitter the staff maintains for him, featuring snark galore.
Mr. Kwong, a teacher in v4. It's very unusual for a non-student to get much attention (either in or out of character), but you'd be hard pressed to find a handler that doesn't like him.
The Godmonster of Indian Flats is more well known from Stuart Ashen's videos than the movie where he's the titular character.
And of course, we have the Excellent Darkhorse himself, Chef Excellence.
The Metamor City Podcast has Artax, originally created as an expository engine to explain some of the more complex bits of the world's magic in universe, the fans have often cited him as a favorite character over several of the main characters.
The Queen of Rogues and Robbers was originally supposed to be a one-shot villain in The Questport Chronicles, but has been brought back every year due to her popularity.
The Engineer from True Capitalist Radio. Many of the trolls who call into the show wish that he would host more than Ghost.
Some of the trolls have gained popularity after the show's renaming to True Capitalist Radio. The Internet Buttstalker, Tub Guy, Ghetto Capitalist, Horny the Clown and the Ban All Bronies guy/Btown also are popular trolls.
Mabaka! has Maruchi, Rokuro's magic teacher. He was almost certainly designed to be a major prick, yet most readers can't help but love him.
Grass Man from Harry Partridge's Bo-Starr and the Champions of Galastrom appears to be a massive fan favourite.
Due to the nature of the show, a case could be made that anyone besides The Narrator Cecil (and maybe his eventual boyfriend, Carlos the Scientist) from Welcome to Night Vale as this. However, the stand-out by far is Tamika Flynn, the brave twelve-year year old girl who led all of Night Vale's children through the dreaded summer reading program, wears a librarian's severed hand as a necklace, and has formed a militia army of children to fight against Strexcorp.
Cecil: If station management is listening, I, of course, hope we find Tamika Flynn and bring her home safely. I hope she finds you first, that is.
In Worm, a character appears once, in the midst of a crisis, a fat superhero who is named only in passing as Chubster, as the casualties are tallied. He remains unconscious throughout his appearance; the protagonist tries her hand at CPR, fails, and she abandons him to die. Despite his unglamorous nature (or because of it?) and lack of dialogue or action, he is repeatedly referred to in the site's comments section, appears or gets a mention in numerous pieces of fanfiction, and is part of several in-jokes among fans.
Velvet Scarlatina showed up in one scene in RWBY and had two words of dialogue, then showed up briefly in another, with no dialogue, intended only to show the prejudice some humans had toward faunus, with no further plans for her. She's now in the main titles of Volume 2 with her (yet un-introduced) teammates and was the subject of a popular contest to design her combat costume.
Grant Kirkhope on Game Grumps. He appeared as a special guest for a grand total of one episode (though said episode was roughly equivalent in length to about six to seven regular episodes), yet he's often considered an honorary Grump by the fans and often appears in fan art. It helps that he seemed to have an innate sense of the show's sense of humor and meshed incredibly well with Arin and Jon.