Looney Tunes has a fairly big history of this. Their first big star after Buddy and Beans The Cat was a minor character in a series of shorts about a group of grade school animals, but his role as the stuttering, somewhat unlucky Straight Man role proved popular with fans and Porky Pig soon became their premiere character. After a few years, a cartoon featured Porky going on a duck hunting trip, running into all sorts of wacky mishaps, one of which was an off kilter duck that only appeared in two scenes (and the credits), put his loony, unconventional antics proved so popular that soon that "Daffy" Duck got his own cartoons and became their next star, until the process repeated itself yet again with their now premiere character, Bugs Bunny.
One of the strangest examples: the nameless drunk cat with the red nose, big lips, saggy jowls, dickie shirt with bow tie and bandage on his tail. He only appeared in the Bob Clampett-directed "Kitty Kornered" as a pet of Porky Pig who teamed up with Sylvester and two smaller cats, but he proved popular enough to appear in many of the spin off series of the 1980's and 90's including Tiny Toon Adventures and The Sylvester and Tweety Mysteries.
Marvin the Martian also fits this only having a handful of short in the Looney Toons canon but ended up becoming the primary antagonist in Duck Dodgers and getting his own music video
Another example would be Taz the Tasmanian Devil. Originally he was only going to appear in one cartoon but he was saved by fans requesting he make more appearances; he made 4 additional cartoons and a major role as a villain in the Christmas special, proving popular enough to get his own TV show. He is now part of the main character rosters and one of the most recognizable characters in the series.
To a far lesser extent, Penelope Pussycat, originally the unlucky nameless cat who would get chased by Pepe Le Pew in his shorts has been gaining her fair share of popularity these days as well.
The Flash was the Ensemble Darkhorse of the original series. In fact, his lack of presence in the first season of Justice League Unlimited was one of the main reasons fans bashed it.
Depending on who you're talking to, Hawkgirl is either an Ensemble Darkhorse or a Creator's Pet.
Lack of Flash is so noticeable that it was identified as the reason why the alternate universe Justice League turned into the tyrannical Justice Lords.
Subverted with Captain Atom, who appeared in the first episode along with other soon-to-be-popular characters, but never managed to achieve popularity. Still, he was able to fight Superman one-on-one and almost thrash the big man, in spite of being a supporting character.
Chernabog and his sequence, Night on Bald Mountain, from Fantasia. Everyone remembers the beautiful pieces of music from the whole thing, but this was the one that stuck to everyone's memory. Everyone that ever watched this was in fear and awe of Chernabog, the sequence is regarded as both so amazing and frightening that it caused the Slavic Satan to haunt many's memories to this day, and it should come as no surprise that, of all the things from Fantasia to put into Kingdom Hearts, they chose Chernabog.
Of its darker sister show Sonic Sat AM, there is Bunnie Rabbot. She arguably had the least spotlight of the main Freedom Fighters, acting as a bit player at best in every appearance, though is popular for her cyborg powers and is one of the few alternate media Sonic characters not to gain much distain.
Scrooge McDuck started as a supporting character in Donald's comics, but eventually became popular enough to be spun off into his own series. Scrooge is much more popular than Donald in Finland and France, where the magazine devoted to Carl Barks' universe is called "Picsou Magazine". (Picsou being the French name for Scrooge). DuckTalesputs Donald on a boat in the first episode, reducing a character that was always going along with Scrooge on his adventures to a guest character. Considering Scrooge started as nothing more than a caricature of thrift in a propaganda cartoon during World War II, that's one escalation.
He didn't. He started out as a Dickensian miser in a Christmas story in 1947. However, most of Donald's relatives and other Disney characters fit this trope. His nephews: started in a Sunday page in 1937 and a cartoon in 1938. Both end with them leaving their uncle. Goofy: started out as a theatre-goer with a goofy laugh called Dippy Dawg in 1932. Gladstone Gander: Donald's (not yet lucky) cousin coming in winter 1947/1948. Gyro Gearloose: started his career with a half-page cameo in a story. And so the list goes on.
Panchito Pistoles and Josť Carioca, Donald's fellow Caballeros, are well-liked among the fanbase as well, to the point that they had a guest appearance on Disney's House of Mouse as well as their own ride (Gran Fiesta Tour Starring The Three Caballeros) in the Mexico Pavilion of Epcot's World Showcase (which was renovated from its former status as El Rio del Tiempo)? Ditto for the Aracuan Bird, who was popular enough to torment Donald in future shorts.
Woody Woodpecker originally debuted as the villain of the Andy Panda cartoon short Knock Knock in an attempt to deliberately invoke this trope-Walter Lantz and his cartoon studio were hitting hard times after the series Oswald the Lucky Rabbit ran out of gas, and Andy Panda wasn't the new hit star they needed badly to rejuvenate the ailing studio. Unsurprisingly, Woody became an instant hit upon debut and went on to immediately star in his own smash hit series of short subjects.
Despite appearing in only five episodes, Cheese from Foster's Home for Imaginary Friends is one of the most well-liked characters, dominating most of the merchandise of the show. This is likely because the target audience is young, and Cheese is The Ditz. Later became a Base Breaker for being given increased exposure and having his goofball tendencies flanderized to Millstone levels.
Invader Zim has Tak. Despite appearing in one two-part episode and having a vocal cameo in another, the amount of Fan-Art depicting her can easily confuse new fans into thinking she's part of the main cast. She had one planned reappearance before the cancellation of the series, but it's certain her popularity would have resulted in many more. Given that she was the first competent Irken we had ever seen, and made a great female foil for Zim, it's easy to see why.
THE MOOSE! Seriously. The Moose has its own fanbase just for being so damn impressive.
And speaking of moose, Minimoose, who only appeared in one episode before the show got cancelled, makes regular appearances in fanart and fanfic, usually as the Woodstock to GIR's Snoopy. He's just so darn cute...
Chomper from The Land Before Time 2 was so popular with fans and critics that he gave him a second Guest Star Party Member role in The Land Before Time 5, this time with a speaking role. This increased his popularity to the point that fans began perennially requesting for him to appear in the sequels that came afterwards. While he never made another appearance in any of the movies, when the TV series was released Chomper was not only brought back, but he became a permanent addition to the main cast.
A lot of tertiary characters have become incredibly popular with fanfiction writers: Craig, Tweek, Pip, Gregory, Christophe (aka "The Mole"), the Goth Kids. Perhaps the most baffling is Damien, the son of Satan, who has spoken in exactly one episode and appeared in the background in a few others. Searching for him on fanfiction.net produces five pages of results, or over a hundred stories.
Damien wouldn't be nearly as popular if slash fans hadn't noticed his interaction with Pip, another example of this trope, in the one episode he was in. If you look closely at those fanfiction.net pages, you'll see that nearly all of them are Damien/Pip fanfics. Which is even more baffling, considering that Damien set Pip on fire to earn the respect of the other boys.
The popularity of the Goth Kids might be because fangirls like to use them as an outlet for their own angst—which is ironic, because that's the kind of attitude the Goth kids are supposed to be a parody of, with them doing it just to stand out and look down on others. Especially awkward since only one of them has a canonical name, though on Fanfiction.net at least "Dylan" for the red-tinged Goth and "Ethan" for the tall one seem to be fanon.
For a guy who is almost certainly gay and has only appeared in one episode and whose only relationship appears to be with Butters (meaning there shouldn't be much for fanfic writers to actually do with him) Bradley from "Cartman Sucks" has quite a few stories about him getting with Butters.
Argent. Despite only appearing for a short amount in two episodes, and subsequently being a very little developed character, there's a large amount of fanart for her, and several fanart groups on deviantART.
There's also Kid Flash, who also only appeared in two episodes. Probably helps that he and Jinx became an Official Couple.
Scruffy was a popular character during the interim when Futurama was not producing new episodes. He only made a few appearances in the original run, and was mostly noteworthy for his extreme apathy. Since the revival, Scruffy has had a much larger role, frequently appearing alongside the main cast, almost solely due to his popularity on the Internet.
A few characters could stake claims to this, though Stacy Rowe is possibly the best example, as her popularity with the fandom was likely the reason why she got an actual, honest-to-goodness recurring subplot in season five, which, for any Lawndale High character not named Daria, Jane, or Quinn, was really quite a feat.
Daria's Cool Aunt Amy, despite only showing up in three episodes (one of which was a cameo).
The Powerpuff Girls featured a one-shot set of villains in season one - the Rowdyruff Boys. They were flat, somewhat uncreative male counterparts to the three main characters. What's more, they were defeated by getting kissed. Mere days after the episode first aired, the Internet was swamped with dozens of fanfics and fanart pieces devoted to them. Entire websites - exhaustive websites, full of art, episode transcripts and bustling forums - were created in their honor. The fans were almost unanimous in the desire to see the boys come back. After four years of demand, they finally returned in season five - given hints of personalities and very strange new hairdos.
Bunny only appeared in one episode, yet is a popular character.
Apu is a good example of recurring Ensemble Darkhorse. First he started out as the typical Indian cashier, and then he got a few episodes centered around him. For Character Development, he even got a wife and eight children. He might also act as the Simpsons' Sixth Ranger, as seen in The Simpsons: Hit & Run.
Both Troy McClure and Lionel Hutz - voiced by the late Phil Hartman - deserve a mention as well, especially the former - before Hartman's death, there were talks about a potential live action film featuring the character. It can't be just a coincidence that the retirement of both characters coincides with the point in the show's history when it developed a Broken Base.
Bleeding Gums Murphy only had a major role in two episodes and a number of background appearances in-between these before his character's death, but his role as a kindred spirit and mentor to Lisa is fondly remembered by older fans of the show (especially those who watched the first season). His death was one of the show's truest Tear Jerker episodes.
Professor Frink was introduced as a wacky Mad Scientist character who wanted funding for his death ray—which Grandpa Simpson talked him out of developing without even trying. He quickly became a regular character. He even had a website dedicated to him before FOX had it removed.
Disco Stu was originally just a one-shot character meant as a joke. Homer was selling a custom-made rhinestone jacket at a yard sale that said "Disco Stu" on the back. When Marge asked who it was, Homer replies "Well, it was supposed to say 'Disco Stud' but I ran out of space." He's since made several appearances.
The same goes for Cletus the Slack-Jawed Yokel and the baby with one eyebrow.
The late Frank Grimes appeared in only one episode and yet is one of the most memorable Simpsons characters ever.
Groundskeeper Willie has priceless moments. He appears fairly regularly, but he had to wait till the 17th season to have an episode which would focus on him.
Crazy Cat Lady for the win! It's amazing what you can do with what is basically an exaggerated character stereotype.
Jessica Lovejoy. Only one episode with a major role. Tons of fans and fanart.
The Music Meister, despite only being the main villain of a single episode. Though, the fact he's voiced by Neil Patrick Harris probably helps. After the episode was out there was tons of fanart, and demands that he be incorporated into the DCU within minutes. The demand for the soundtrack was so high that they announced plans to release a soundtrack about two or three days after the episode leaked onto the Internet, and said that if the show had a third season he would be back. (Unfortunately, he wasn't.)
Two-Tone is without a doubt the most popular Dalmatian in the series, in fact so popular that fans felt she deserved to be the fourth main pup instead of Spot. She's mainly popular for her unique spot pattern and tomboyish personality. She usually appears in the background in most episodes but has had some speaking parts in a few episodes. Her claim to fame was the episode, "Love 'Em and Flea 'Em" where she played a major role and was in a romantic relationship with Lucky. Also, being voiced by Tara Strong just adds to her popularity.
In a similar fashion, Patch has become quite popular despite looking much differently than he does in the movies. Most fans prefer his movie design because it's cuter, but others prefer his series look as it is closer to Dodie Smith's depiction of him.
Tripod has a fairly large fan base, namely for being a Handicapped Badass. A lot of fans like to pair him up with Cadpig (the general reason being that the two would likely bond over their physical shortcomings and insecurities interpreted by the audience), despite the fact that neither of them conversed with each other at any point in the series.
Mooch, the farm bully, both loved and hated by fans alike. Another character that fans like to pair up with Cadpig since they were both in a romantic relationship in the episode, "My Fair Moochie" (even though Cadpig was only pretending to be his girlfriend.)
Wizzer and Dipstick both seem to have a lot of fans. Often depicted as bullies since they're usually seen hanging out with Mooch. They're also well known for having big parts in the live action films and the video games.
As a one shot character, Blaze has also been a subject of Cadpig shipping, except in this case, Cadpig did show some genuine interest to him (such as calling him a "hunk" and batting her eyelids to him). It also helps that Blaze is a Nice Guy with amusing acting talent.
Ivy, Cruella's niece, is the single most popular antagonist, even though she only appeared in three episodes.
Amber, Anita's niece, has gotten quite a cult following for a one shot.
The Dalmatians' hero, Thunderbolt, has an impressive fan base of his own outside of the universe. Some have even gone as far to make fan made girlfriends and wives for him.
Even though he was only in 101 Dalmatians II: Patch's London Adventure and not in the series, Thunder's sidekick, Lil' Lightning has also gained a cult following.
Jewel is a Dalmatian pup who did not appear once in the series, but she has appeared a lot in fan art with a particular fan depiction. Fans speculate that if Jewel was a character in the series, she'd have a valley-girl-like personality.
Pretty much every Dalmatian pup with a name who didn't appear in the series has a fan base of some kind (e.g. Penny, Pepper, Freckles, Fidget, etc.), Penny especially, considering she had a fairly big role in the animated movie and was originally intended to be one of the main pups in the series (in some countries, she's in place of Cadpig).
Angel from Lilo & Stitch: The Series, an intended one-shot who reappeared later due to popularity. Not to mention Sparky as well as some other experiments.
Charity Bazaar from Histeria! is stated to be the best character on the show by even people who hated it.
In fact, in the Histeria! fandom, the whole Kid Chorus seems to be more popular than the hosts (with the exception of Miss Information).
There's also Jun, which the creators even commented on. Likely why she reappears in the Grand Finale.
Both Suki and Jet were meant to be one offs as well. Fan demand brought both of them back in substantial parts and Suki even joining the gAang.
Jin as well. She appeared in one episode in Book 2, where she went on a date with Zuko, and had a cameo when Ba Sing Se fell. You wouldn't have any trouble finding fan art for her, and there is a fairly strong following for the Jin/Zuko ship.
Although it's not exactly as much "popular" as "well-remembered", Koh. He barely had any plot-importance even the two times you see him (one was a flashback), but he's was just so damn creepy that he's become a frequenter of fanworks and Epileptic Trees all the way up to the end of the show.
Harley Quinn was introduced as a goofy bit-player, but hit it off so well with both the writers and the audience that she became a regular and a Canon Immigrant.
The series was also responsible for the rise in the popularity of villains like the Mad Hatter, Clayface, and Mr. Freeze, who until then were practically obscure to people who weren't into the comics. Special mention to Mr. Freeze's case, as his backstory in the animated show was so well-written that it won an Emmy. It was also adapted into the comic book series and turned him into another memorable villain of Batman.
"Thriftie", an unnamed character with only one minute of screen time.
Roxy Rocket only appeared in two episodes (one of which was only a cameo) and yet has gained a strong enough following to become a Canon Immigrant.
Arguably the penguin with the most fans is... Kowalski. Uh huh.
In The Animals of Farthing Wood the most popular character is Bold, Fox and Vixen's oldest son. After a reckless attempt on Scarface, he leaves White Deer Park to live his own life. He learns the hard way how to provide for himself, gaining a partially blind eye and a bullet in the leg. He struggles to earn the love of a vixen (Whisper), who only becomes his mate after finding out his father is a figure of local legend. He swallows his pride and takes her back to White Deer Park so she can have their cubs in safety. The injury in his leg ultimately kills him, but not before he knows his father is proud of him. And he only appeared in eight episodes of a three season series.
Roger from American Dad!. This was probably inevitable given his diva personality.
Principal Lewis, for being the most outrageous character other than Roger.
Ms. Doombringer, a highly competent fairy hunter that appeared in just one episode but has people asking for more.
Molly, a girl that showed up for one episode but already has shippers pairing her and Timmy together.
Also Remy Buxaplenty to some degree - he appeared in one episode to challenge and lose to Timmy in a duel, and disappeared after that. All the same he had a fairly significant following and a tendency to be shipped with Trixie Tang - who wasn't even in the episode he was in - and years later was brought back for a small handful of new episodes.
Dark Laser. Initially, he was a one off villain. Then he made an appearance in the fifth season as a continuity nod, but by the sixth season, he'd become a semi-regular, even having a major part in the season finale.
Anti-Cosmo is quite popular among the fandom, especially the idea of Timmy being his godchild. No wonder Foop is The Scrappy.
In Metalocalypse, a show about the five members of a death metal band, who emerged as the most popular character? Their manager, Charles Foster Ofdensen. Fending off an assassin and making said assassin stab himself helped.
Fred the Barber Half the show's references on this site are about him. He was the least dangerous but most memorable villain.
Di Lung. To the point where he would appear more frequently during the later seasons.
Katz is another example. His popularity may be the reason he appears more often than other villain on the show.
King Ramses' is quite popular despite the fact that many find his episode to be the scariest. In fact, the reason as to why most people assume he is scary is possibly an excuse to make him seem more popular.
Noah. His popularity is all the more astonishing considering his extremely limited screentime in season one - he appears in just six of the twenty-six episodes, has no lines in three of those six episodes, and has two words of dialogue in the entire second season, aside from the finale. In response to his popularity the producers added him to season three, with Chris introducing him as a "returning fan-favorite".
Likewise, Cody's popularity in season one is why he was given a major role in World Tour, even managing to reach the final three.
Also from Total Drama Revenge of the Island, Dawn. Seriously, after the first trailer for the series aired, she had more fan art on Deviant ART than any of the other cast and was the first to have her own fan group there. Even now that the season has aired, she's still quite popular.
Jasmine. Despite appearing in a minute-long clip, she had quite a large amount of fanfics about her in which she becomes a contestant.
Samey. She was only in five episodes, and is now probably the most popular character of the newest season.
Mal. Dear God, Mal. Go look up Total Drama on Deviantart.com and Fanfiction.com. See how many fanarts or fanfics that are not about him. It's like finding a needle in a haystack.
Misery is far and away the most popular character on the cheerfully-gothic Canadian cartoon Ruby Gloom. Her only conceivable rival is the title character, at which point it's kind of hard to draw a comparison.
Gene Khan in Iron Man: Armored Adventures. Yes, even after the season one finale and what he did during it. He is the Ensemble Darkhorse of the fandom. Two of the longest Fan Fics in the IMAA fandom focus on him. Fans like pairing him up with Tony and Pepper. The fan forums' Epileptic Trees tend to center around him quite often. His mother also gets discussed/written about quite a bit given that we only see her in a single flashback once.
Cad Bane earns this role as a badass villain with a western motif. Captain Rex has his fans too.
As does Admiral Trench, the chessmasterspider who turned up, much to the surprise of Admiral Yularen who thought he was dead, made Anakin run behind the moon for cover, then bombed the planet to draw them out and deduced who was flying the retaliating stealth ship. When he died the first time it was at the hands of a special task force just for him and led by Jedi.
Embo, the bounty hunter. After appearing in only one episode. This video demonstrates why. This led to him appearing in more episodes later on.
Savage Opress has proven to be quite popular, partly due to his resemblance to fellow Ensemble Darkhorse (and his brother) Darth Maul.
Hondo Ohnaka. He was supposed to be a one-shot villain, but was brought back twice in season two and then appeared in three arcs in season five. All in a row. You want to know why? THIS IS WHY.
Despite his scant role in Code Lyoko, Clone William's calm idiocy and "adorable" personality made him a hit with fans- even moreso than William himself.
Also, Dr Hutchison who was only a one time character that had so much appeal, that she married Filburt who was one of the main characters.
Filburt himself is an example of this trope. He started out in the series as a minor, nameless character that would appear every now and then, but eventually became one of the main characters.
Peaches, the ruler of Heck, who appears in two episodes.
Adventure Time has Marceline the Vampire Queen. She was already intended to be a recurring character, but after her first appearance she was already a fan favorite. She seems to show up more often now as a result.
Lumpy Space Princess. "Bunch of smooth poseurs."
Adventure Time with Fionna and Cake caused a massive influx of Marshall Lee and Lumpy Space Prince fans, even though they only appeared for about four seconds and didn't even have any lines.
"Fionna and Cake" in general. The episode got 3.3 million views, while most other episodes get 2 million something views. If you search "Adventure Time" on Deviant ART, you'll get nearly as much fan art of the gender-flipped characters as the regular ones, and fans have even made some of their own gender-flipped versions of characters that didn't have one in the episode. There's probably even quite a bit of Finn/Fionna and Marshall Lee/Marceline shippers out there. And these characters were just part of Ice King's fan fiction.
Marshall Lee. The gender flipped version of Marceline only showed up for a few seconds in the episode, and had no speaking lines. For well over a year since his appearance, he has skyrocketed into possibly the most popular character on the show.
The weirdest thing about it is that if you do a deviantART search on Adventure Time, the most popular piece of art that comes up is gender-swapped.
Even Flame Princess was more popular by the fanbase being the alternate love interest for Finn, but with only 15 episode appearances. She would've been great in her role as one of the main characters too, like Finn, Jake, Ice King, Bubblegum, LSP, and Marceline.
Ducky Momo has a lot of fans, considering how little he is in the show, and that more as a concept than an actual character. His popularity is no doubt due to the TearJerker song he's introduced with.
Gretchen (the Fireside Girl with glasses) gets this sometimes, mostly because she was the first girl the boys' age to get a name other than Isabella, and thus became Ferb's designated love interest for anyone who didn't like Ferb/Vanessa. The fact that she is later revealed to be rather brainy (like Ferb himself) seems to retroactively justify this. The other Fireside Girls get this a bit too.
In the episode "It's About Time!" there's a kid who helps Candace sneak back into the museum after being thrown out for yelling. He only appeared in that one episode, and he probably doesn't even have a name, but he was such an interesting character that some fans want him brought back. Also, he stole a complete fossilized pterodactyl skeleton from the museum.
An example of a team of Ensemble Darkhorses are the Brotherhood of Mutants. Particularly Quicksilver and Toad. While they as a whole get it for their status as Ineffectual Sympathetic Villain, the Fan Dumb tend to be very touchy on this. While undoubtedly entertaining and easily popular, they have a habit of being latched onto by the crazier fans. Especially Avalanche and Quicksilver.
Canon ImmigrantX-23 was so popular that she was brought into the comics after only two real appearances and a cameo in the finale, with a million fanfics dealing with her life.
The show has a notable exception among the franchise: Wolverineisn't the most popular character on the heroes side. There actually isn't just one in particular. The show was so well written than almost anyone could function as the Ensemble Darkhorse, and if you look at the fandom that's what happened, but special mention on the good guys side should go to Nightcrawler. This is about as close and any adaptation got to his original playful, charming, character from the comics.
Nightcrawler is easily the most popular male of the main cast and the most popular female character in the show is Rogue.
Marie, the blue-haired Kanker. She has a much larger fanbase than any other girl in the show and is often considered to be the most attractive one, despite not being intentionally designed as such. Pairing her with the object of her affections/psychosis, Edd, is probably the most popular 'ship in the fandom. Her sisters get this to a lesser degree, as does Rolf.
Plank. Fans who have made stories focusing on that piece of wood make him out to be secretly an evil genius due to apparently being sentient and being only able to "talk" to Jonny. Also, there's a plushie of him◊.
Generator Rex has Breach, who gained a bunch of fans due to a combination of some Foe Yay with the main character, and being attractive while being delightfully creepy at the same time. It got to the point where the fandom had a collective freakout when she seemed to be killed off, then rejoiced when it turned out she was fine.
21 and 24 (but especially 21 now) from The Venture Bros. They started off as nameless henchmen (numberless, too in the first episodes) to have more air time than the Monarch himself. In the latest season, 21, after he Took a Level in Badass, could arguably be called the leader of the Monarchs. The other henchmen refer to him a General 21. He is even putting the moves on Dr. Misses the Monarch, whom he has always crushed on.
An interesting case occurred during production; the three fairies were originally intended to be minor supporting characters, with no names and no differences between them other than the colors of their clothes. The filmmakers became such fans of the characters as they developed that they wound up taking over the film.
Maleficent, the movie's Big Bad, is also popular and well-remembered. She's even getting her own live-action movie in 2014.
Despite the frequently horrifying content, the Peadofinder General in Monkey Dust is particularly popular. Something about the big hat and green skin...
Ultron first appeared in episode 5 as an innocent prison guard. As the first season progressed, he gradually entered the foreground while obtaining the knowledge that would turn him into the Killer Robot Marvel fans know and love. He finally turned against the Avengers in episodes 22 and 23, performing such feats as possessing Iron Man's armor, seemingly killing Thor, and using stolen nuclear missile codes to try and wipe out all "flawed" life on Earth. Even though the Avengers defeated him in only two episodes, an unofficial poll deemed him the most popular villain by a longshot.
Doctor Doom won fans over even before his first episode premiered. His actual feats didn't disappoint either; he overcame six Avengers and the entire Fantastic Four in a battle, and found a Skrull among them even before they could. Doom did another guest spot 10 episodes later, in which he helped Iron Man create a weapon to expose disguised Skrulls. Doom explained that he spent so much time trying to prevent the Skrulls from taking over the world so that eventually, he could take it over instead.
As Iron Fist and Luke Cage beat up thugs, cracked dry wit, and helped track down the thief of Hank Pym's Ant-Man suit, the viewers wished they could watch these Heroes For Hire kick even more ass in their own show.
Word of God is that Dr. Drakken and Shego were originally just supposed to be a part of the show's rotating cast of villains, but became so popular with the fans that they were used more and more often until they became regulars. They eventually hit a point where they not only were the most fleshed out villains in the series but also began having recurring bouts of Enemy Mine, and then came the Grand Finale of the show where they actually become key players in saving the day.
Electronique was rather popular with fans, more than you'd expect from her single appearance. But then, she was a Baroness and Gadgeteer Genius with electrical powers, a short temper and a hammy accent from somevhere in zer centre of Europe, so she was a memorably entertaining character, and as a villain in Shego's hometown she had a connection to the fandom's favourite character.
Doug: Roger Klotz and his gang, the chief antagonists. Also, Doug's older sister Judy Funnie.
Maximus IQ from Atomic Betty: Despite him being a villain, people see him as a main character as well.
Initially only appearing once in a series with Quarter Hour Short episodes, Ultraprison's Mistress became surprisingly popular among the Superjail! fandom during its first season. She managed to return at the end of the following season, played a role in the third season premiere, and fourth season premiere involves Ultraprison yet again.
Charise also receives this treatment, due to her relationship with Jared and being seen as cuter and innocent compared to Mistress and Alice.
Cornchip Girl, Butch, and Lawson also have sizeable fanbases.
Miss Grotke, for being a MoeHippie Teacher with hints of Sensei-chan here and there (and was pretty popular among the show's older male fanbase)
The "Bad Kids" consisting of Conrad Mundy, Greg Skeens, Sue Bob Murphy, Kurst the Worst, and Lazy Kid are quite popular despite only having large roles in a few episodes. It isn't too hard to find fanfics with these guys in it.
Fillmore! had a red-herring character in one episode named TQ in one episode; a stoic, Deadpan Snarker Zen student. Apparently, he really caught on with fangirls.
From Jem we have Stormer in the Misfits. Her popularity is fueled by her being the Token Good Teammate of the Misfits, albeit she is capable of having a nasty attitude from time to time. She's the overall creative force behind her band but she never gets credit for it, and usually winds up helping (secretly) the Holograms when she absolutely feels she needs to. Stormer has also been the only Misfit to be offered a place in the Holograms, but she turned it down because she felt the Misfits needed her more. Word of God has it Stormer's first loyalty is always going to be the Misfits regardless, which really only makes her more likeable; she sticks by her friends.
Jade's (technical) Superpowered Evil Side, the Queen of the Shadowkhan. Despite only showing up in one episode in Season 2 (and getting a brief mention by Tarakudo in Season 4), there are quite a variety of stories in which she regains the powers and/or personality of the Queen. (See Project Dark Jade.)
The Demon Sorcerers also count, though not to the same extent as Queen Jade because they got more screentime. They were a Big Bad Ensemble in the second season, but were never heard from again after their defeat. The fandom loves these guys, who were each given decent and distinct personalities despite only really getting one episode each, plus a few group appearances.
In particular Hsi Wu, the sky demon. Somehow the one episode he has a significant role in managed to make him a fan favorite for shipping with Jade. Or else everyone just hates Paco that much...
Tashy 497, a lovable squishy space squid who showed up in a single episode with the same name. Apparently, he was so adorable the fandom kept him, and now he has his own fanart, almost as much as anyone else, including the main cast. He often will make a cameo in other artworks, but never in series, because it ended and he died before the episode was over. 20 minutes screentime.
Xeexi. 2 minutes screen time.
Barb. She walks into their house on random, and has reached a supreme stalker status, even though she was only ever used to move the story along. Her stalker status came from her various intimate, and arguably sexual, encounters with Mr.Lunis. She's often depicted in fanworks as the creepy neighbor. So this is the one time where the fans keep a character IN character. 5-10 minutes screentime.
Mirabel. Mentioned because....there really is no reason why. She's just commonly mentioned. Went to the prom with Lance, then he left so she spent that time with Jason. Her popularity may have stemmed from people settling that Ilana was free again because Jason and Mirabel hit it off, even though that was never confirmed. minute and a half of screentime.
Kristin, the goth girl introduced in Ballad of the Scary Mary and asked out by Lance is Under the Three Moons. Because her potential was never completely reached, and because of her cool attitude, she became someone the fans noticed. Also rocketed in fandom for the same reason Jason is: She ruined the Lance/Ilana ship. Depicted in fanworks as a snarky, kickbutt, female Lance. Also popular because of an episode of Dexter's Laboratory, Eye Eye Eye's, where the little girl depicted looks like a younger version of Kristin. Now she's known as the Eye Eye Eye's girl. About 2 minutes of screentime.
The Eye Eye Eye's episode of Dexter actually made another character popular; Brandon. "Kristin" ran off with a brown haired boy with shining eyes, and he looks like a younger version of Brandon. And so the ship "Krandon" was born. His popularity also comes from his jerkish behavior towards Kimmy as his Ex. 45 seconds screentime. Both Titan and Dexter were created by Genndy Tartakovsky, justifying this assumption.
Todd has become popular due to a stellar performance by an avid RPer who took his little 30 second run and made an interesting character. Even though it was never said in the show, he says "fabu" alot in fanon, is bisexual, and looking for love.
Baron (arguably the biggest example of this on Titan's listings) from the episode Shadows of Youth has become popular enough to be shipped with Ilana, have his own fanfics, and many wanted him to show up again. In fanon, he grew up to be a sexy, yet confused, bastard who loves to torture Lance in his every day life, part of that being flirting with Ilana. He's actually blown up so much that him saying "I WAS SUPPOSED TO BE A PLOT DEVICE" has become a meme, and exploited for the fans to hold up their campaign. Part of the reason fans fight hard for this show is Baron, figuring out what happened to him, and the fact that you can't have such a jerk character who was depicted only as a child then never get the opportunity to show his later years and have no one wonder where he went, so his Darkhorsism is justified. 10 minutes screentime.
Mike Chan in "Roar of The White Dragon". Often depicted as the self centered, jerky, somehow sexy, Asian. Paired with Lance at times, even though Lance already outwardly expressed that he was in love with Mike's Car, but hated Mike. Might be popular because it was alluded that he would come back, but the show ended before he could. 12 minutes screentime.
His girlfriend, dubbed June by the aforementioned RP'ers (There is an official RP that does show cases on CN's facebook page with a well written out script, that is why they are so acknowledged and important in this fandom)even though she never said anything. And that is what she is known for. Not saying anything. 5 seconds screen time.
Meat. Popular because he was voiced by Bill Fagerbakke (Patrick Star). His wacky antics and nonsensical dialogue made him popular, and is often depicted doing something silly and out of place for this show. Also depicted as Octus' best friend even though he only had about a minute of screentime.
The other cheerleaders. Monica (the black one) is known for only talking about how hot Lance is, Amber is known as Kimmy's closest BFF who's not all that bright (likely brought about on her from the fandom because she's blond) and obsessed with her weight. Justified due to her freaking out and thinking an airway would break because she had eaten a single fry at lunch, and Tiffany, who is best known for not being known. At one point, people only noticed Amber and Monica, but when people started scratching their heads to remember the other one, when she was remembered, they remembered hard. Various amounts of screentime, but no more than 10 minutes.
Despite being by far the most obscure member of the original cast, Artemis has proven quite popular with fans.
Even though he only appeared in a few episodes, Klarion the Witch Boy has a sizable fanbase with a good amount of fan art devoted to him.
Nuka and Vitani have relatively minor roles in The Lion King sequel, yet have become the favorite of many fans likely due to their unique designs and obscure backstories (or rather a lack of).
From Codename: Kids Next Door, Sector Z! After five minutes of screentime in the movie they won the hearts of a sizeable portion of the fanbase with their badassery. It probably helps that they were the Delightful Children from Down the Lane before they were Brainwashed and Crazy.
Albedo, a Galvan who turned into a Palette Swap of Ben, is popular among the fandom, despite lack of appearances.
Ben 10 is a specific case in that the main character himself is technically an army of Ensemble Darkhorses. Indeed, Ben Tennyson being a shapeshifter who can assume various alien forms, across the series he gets a lot of forms that are heavily popular amongst the fans even when not playing an especially major point in the plot or even having limited appearance:
While Ben 10: Ultimate Alien has been criticized for adding many Replacement Scrappies of old aliens, the five Andromeda aliens dubbed as "Team Awesome" by the fans are usually recognized as good aliens. The fact they were scanned from actual characters with each one their own stories probably help.
Aside from the aliens forms, several minor characters and villains in both series have become Ensemble Darkhorses. Those include Charmcaster, Lucky Girl (though this is actually Gwen is disguise), Kevin (who later was upgraded into a main villain and then a hero), Albedo, Darkstar... and Paradox is probably as popular as Rath himself.
Articguana and Buzzshock, two of Ben 10,000's aliens, became rather popular, with fans wanting to see them be unlocked. The fans got their wish with Articguana, who finally got used in Omniverse, and Buzzshock a couple of seasons later.
While most of the pups in the show were intended to be one-shot characters, some have gained some big fan bases. For instance, the puppy known as Pepper became a mega fan favorite (most likely because of her tough girl personality) so much that she was brought back in a Season 3 episode working with the Super Secret Pup Club.
Lucky's father, Slik, has an impressive fan base, mainly due to his striking resemblance to Tramp from Lady and the Tramp.
Cupcake started out as a dark horse. Everyone (both the fans and the show's creators) found her to be so cute that she quickly became a permanent recurring character starting in Season 2, except with a more down-to-earth personality rather than an innocent cute kid.
Lucky's owner, Dot, introduced in the Season 1 finale, has become likable enough that she would recur more often in Season 3.
Lin Beifong, the daughter of Toph from the original series. At first, her stern, no-nonsense attitude didn't attract many fans, but her popularity shot into the stratosphere following her Heroic Sacrifice to save Tenzin's wife and children.
Commander Bumi only shows at the very end of the finale, screaming like a maniac (just like his namesake). The fandom loves him. His expanded role in Season 2 only deepened that love.
Tarrlok, whose Murder-Suicide of him and his brother Amon/Noatak has cemented him in the fandom of an Alas, Poor Villain. Many fans wish that he had lived and would have been able to undergo a redemption arc since it was obvious that he wanted to rise above the ghost of his father in his life.
This has even hit a background character with no name who is long dead, specifically an overweight Airbender Avatar with a marked resemblance to a Laughing Buddha seen in the Spirit World. He is, of course, the most powerful Avatar to ever live.
Iron Fist is notable for being one of the few main characters to not be The Scrappy: he is less a jerk to Spider-Man than the others, he has an actual personality, and his origin actually is mentioned and shown.
Doctor Octopus; this version is outright creepy, has a developed and credible Jerkass Woobie backstory, is effective in a fight, has a good design and voice (even more impressive considering he is played by Tom Kenny!) and possessed an actual story arc that has him evolving. He seems to be the only dark and mature element so far that made it in the show.
Taskmaster and Beetle, being both portrayed as Bad Ass, menacing and truly competent, got quite good reception amongst the fans;
And so far, episodes involving other key heroes such as The Incredible Hulk, The Mighty Thor or Iron Man got good reaction as well due to being faithful to their most well-known incarnation, especially Iron Man.
Also, for those not mad about the change Harry Osborn is pretty popular since the idea of him being Venom is a different and interesting twist. The fact he also is pretty much possibly the nicest version of Harry Osborn in all animated adaptations may help as well.
Even those who dislike the show tend to admit the janitor played by Stan Lee is an enjoyable part in the show.
There's a reason why Phil Coulson appears in this show.
The show's portrayal of Deadpool was naturally extremely popular, with many considering his episode to be the best episode of the whole series. It helps that the episode was written by Joe freaking Kelly.
Yuck from Yin Yang Yo is the evil counterpart of Yin and Yang whose both a Manipulative Bastard and a Jerk Ass. He only appears in six episodes total throughout the whole series yet that doesn't stop him from having a much larger fanbase than the main characters. Though other villains such as Carl and Smoke are fairly well liked, he is arguably the most popular. His Foe Yay with Yin in "Falling Yin Love" and Heel-Face Revolving Door in "Upstanding Yuck" only add on to this.
Care Bears: Baby Hugs and Baby Tugs started out as dark horses during the early days of the franchise. However, a majority of the Nelvana TV series is focused on them.
Cheryl Tunt from Archer is popular with the fans for being a hilarious and surprisingly well-developed Cloud Cuckoolander.
And Doctor Krieger: Equal parts Q from James Bond, textbook Mad Scientist and horny 17-year-old stoner.
Mona Lisa, a girl mutant from Teenage Mutant Ninja Turtles (1987), appeared in just one episode in Season 4 as a potential love interest for Raphael. She remains one of the more popular side-characters.
Simon Belmont, despite being rather Out of Character, has gained some popularity if only because he seems to be the only main protagonist with any sort of personality. Being a constant Butt Monkey probably helps this, too.
Gameboy is a bit of a Base Breaker, but there are plenty of people who seem to like him.
Mike, a former friend-turned-bully of Kevin's, only shows up for one of the earlier episodes (sort of; it's really a robot modeled after him), and yet he seems to be well remembered by the fans.
The Scotsman from Samurai Jack: a big, loud, barrel-chested walking stereotype with a huge Scottish claymore and a machine-gun for a leg who picks a fight with Jack for no real reason at all. Usually when a baddie does this he's curb-stomped by Jack in one blow, but fans were shocked and delighted when The Scotsman instead evenly matches Jack, fights him for a straight day, and the battle ends in a tie when they are both too exhausted to continue. The guy went on to return in a later episode, then gets A Day In The Lime Light episode where he saves Jack's life repeatedly over the course of a two-part episode.
The Amazing World of Gumball has a few, namely Nicole (if this very wiki is anything to go by), Tina, Rachel, and Carrie. Generally most of the secondary female characters are this in the fandom.
Pizza Steve from Uncle Grandpa, though given his personality is it any surprise?
If you ask a fan of The Magic Adventures Of Mumfie what their favorite character is, they will probably say "Scarecrow". He's such a beloved character that people who've seen the show as children refer to other people as "what-iffers".
The Heffalumps and Woozles from The Many Adventures of Winnie the Pooh. Canonically, they only appeared in one 3-minute musical segment and were never mentioned again within the film. In addition, they have rarely ever appeared in the Disney Crossovers and for the ridiculously few times that they were, they were just a pass-by halloween segment or mooks at best! Despite this, they have gained love (and/or terror) from fans of every shapes and sizes due to the segment's love of anything that comes out of a LSD hookah.
A lot of people who are not big fans (or are haters) of the franchise tend to favor Eeyore. His gloomy, pessimistic personality and the fact that he's a little bit of a Butt Monkey make him stand out amongst the rest of the characters.
Probably the most overlooked character in the whole franchise is Gopher, a character who is very humorous and likable. What makes him so unique is the fact that he was made specifically for the Disney franchise and was not from the stories by A.A. Milne (he even jokes about it by saying, "I'm not in the book.")
Littlest Pet Shop (2012) gives us Sugar Sprinkles, the stoner-esque cat who lives in the Sweet Delights truck. After appearing in a single episode in season one and getting as much fan attention as the main pets, she came back for a single episode of season two, as well as another episode appearance in Season 3.
Fans of The 7D have proclaimed that the Glooms are the "real" stars of the show.