In the shorts, Fenneko became massively popular for her deadpan comedy delivery. This has since lead her to become a bigger player in the Netflix adaptation.
Haida is likely the most popular character of the series since the Netflix Adaptation. His endearing personality, his unlucky romance with Retsuko and the comedy and cuteness he brings to the show have made him gain increasing focus through the seasons, with Season 3 basically putting him in the Deuteragonist role officially.
Attack on Titan's Levi is beloved by the fanbase, even more so than the main characters. Thanks to his incredible fighting prowess and ability to curbstomp some of the strongest Titans, along with his monotonic insulting voice, Levi started appearing on just about every piece of AoT merchandise, got his own light novel spinoff, and most likely will stick around as one of the franchise's most popular characters.
Heavy Cruiser Takao from Arpeggio of Blue Steel proved so popular that along with Iona she's pretty much the face of the series (from promotional materials, you'd be fooled into thinking she was the main character). In fact, her massive popularity surprised even the manga's creators and they had to radically change their plans for her as a result. It's gotten to the point that she even has her own spin-off (Salty Road), which chronicles her misadventures while she's separated from the main plot.
Fan favourite Dazai Osamu in the anime adaptation of Bungou Stray Dogs, where he has almost as much screentime as the protagonist, Atsushi. It even adapted his light novel-only backstory, taking up four entire episodes (of twelve) of the second cour.
Accelerator was a villain who slaughtered 10,031 clones and was eventually stopped by the protagonist, but he was so popular with the fanbase that he was given a chance to atone for it. Ever since then, he's become one of the three protagonists of the series. He later got his own spin-off series, A Certain Scientific Accelerator.
Then there's Junko Hokaze, a supporting character for Misaki Shokuhou (herself a secondary character in A Certain Magical Index and A Certain Scientific Railgun). Despite starting out in such a minor position - for a long time even her name wasn't revealed - she was popular enough to get a spinoff of her own, A Certain Scientific Railgun Gaiden: Astral Buddy.
Code Geass: Jeremiah Gottwald was supposed to die early in the series' run, but proved to be so popular that he was allowed to survive and become a more important character than originally planned.
Kurumi in Date A Live. Although she was always intended as a major character, being one of the Spirits around which the plot revolves, she is arguably the series' most popular character. She has her own spinoff Date A Live Fragment: Date A Bullet.
Ai Haibara. Introduced later in the manga than other characters, Ai quickly became one of the most important characters in the series, and gained more screentime as a result. She is also very well-loved by fans thanks to her personality and the Ship Tease with Conan.
Tooru Amuro. He was introduced Chapter 793 of the manga but since then gained a huge fanbase on his own. He now has his own Spin-Off manga and a movie with him as the central character.
Doushitemo Furetakunai: Onoda, the best friend of the main characters, was a popular enough character that the author mentions in her notes that it is the reason why there's an entire spin-off focused on him set a little while after Shima and Togawa get together and Onoda realizes he is interested in Shima.
Vegeta was originally supposed to be just the Big Bad for the Saiyan saga, but proved to be so popular among the fans that Toriyama continued using him and turned him into the Anti-Hero as a result.
Frieza. He is often cited as one of the best and most important villains in the franchise. His popularity has reached such a point that is remembered on several occasions, including in the film Battle of Gods. He would later take center stage as the villain of Dragon Ball Z: Resurrection F, and then brought back for the Universe Survival arc of Dragon Ball Super.
Speaking of Battle of Gods, the movie's antagonist, Beerus, has become a recurring character, with him having an important role in the story of Dragon Ball Xenoverse: the first Dragon Ball Z game to feature an original story in a while. He also plays a role in the next movie Resurrection 'F'. He also plays a role in Super as pretty much the main character.
Cooler is a breakout movie character, and shares his brothers' popularity. He is the first Non-Serial Movie villain to be brought back for a second film and appears in a large number of Video Games and fan work. The fact that he is a Benevolent Boss, a rarity for a Dragon Ball villain, sure helps.
Bardock, father of Goku, was an anime creation for a special going into detail the events that led up to the destruction of Planet Vegeta. The special was well received, and Bardock was actually so well liked by Toriyama that he actually included him in the manga. Years down the line, Bardock became more heavily featured in the video games and eventually got a spinoff manga and OVA where he got to turn Super Saiyan too.
Future Trunks was a well-received combination of badass and Pretty Boy, but was only featured in one arc. To compensate, he was given his own origin story film and allowed to star in several non-serial movies, and Dragon Ball GT had present-day Trunks at the same age as Future Trunks as one of the main characters. He later got his own Spin-Off game Shin Budokai: Another Road, which wasn't very well received, but then became the Deuteragonist of the much more deserving Dragon Ball Online and Dragon Ball Xenoverse, complete with a new sword. In Dragon Ball Super, he gets his own arc and an unique transformation.
Mavis Vermillion from Fairy Tail. Right out of the gate from her introduction, she was loved for being a Little Miss Badass with an amusing personality, and frequently being a topic of Wild Mass Guessing in the series (especially with her implied connection to Zeref) only increased interest in her, until she became a central character in the series starting with the revelation that she's a Living MacGuffin in the Tartaros arc. Eventually, she received her own Origin StorySpin-Off called Fairy Tail Zero, which itself became so popular that it received its own anime adaptation. By the time the Alvarez Empire arc rolled around and her tragic history with Zeref was revealed, she's gotten almost as much screen time as the main characters.
For Hayate the Combat Butler, Hinagiku Katsura is pretty much the most dominating force in the series. In both official and unofficial popularity polls, she has routinely trounced the entire cast - she was once only a dozen or so votes short of beating second, third, and fourth place combined. It was considered a huge upset when a character in the third official manga poll actually got just half the votes Hinagiku got. In addition to a lot of character development and truly massive amounts of Ship Tease with Hayate, Hinagiku has become more woven into the serious plot of the story and her birthday arc gave her one of the longer and more emotive story arcs of the manga. By now she is considered a main character in her own right and is the go-to character when Hayate needs help.
Hinagiku managed to be the most popular character of the first anime as well despite it having little relation to the manga and keeping her in a supportive role with much more focus on the wackier characters of the series. The second anime even returned to the manga story to cover her birthday arc, with her VA Shizuka Ito getting to sing the ending theme. It's since been pretty much a tradition to use Hinagiku and her Will They or Won't They? with Hayate to market for the series, even for the movie and third anime where she was left Out of Focus. Her one episode in the third anime had the characters saying it was the episode all the fans were waiting for. The fourth anime even went so far as to have Shizuka Ito sing the opening theme with the animation essentially billing Hinagiku as the main character, appearing more than the actual main characters and beginning and ending with her, and she was given scenes that weren't in the chapters being covered.
Generally, if there is merchandise of a character, Hinagiku's version always comes out first or there only exists a Hinagiku version of it. While every character got one or two image songs for the anime, Hinagiku got that and three full character albums with Shizuka Ito even doing special live performances and doing a full cover of Cruel Angel's Thesis inserted into the episode where Hinagiku had to sing it in the manga. The actual Idol Singer introduced later in the series only got one after Hina's third album came out, and both were given a Crossover album with The World God Only Knows (represented by their Tsundere and Idol Singer Haqua and Kanon).
Despite the firsttwo Parts of the series not being all that well-known to the general public, Robert E. O. Speedwagon still remains not only the most iconic character of the Parts, but also one of the most iconic characters in the entire series. This popularity eventually led to him returning as one of the main characters of Eyes of Heaven.
Rohan Kishibe from Diamond Is Unbreakable is possibly the only supporting character to be more popular than the Part's protagonist, eventually leading to him getting his own spin-off manga.
KonoSuba has Megumin. Originally just another quirky addition to Kazuma's party, Megumin's cute design, chuunibyou personality, and meme-worthy quotes allowed her popularity to skyrocket past every other character, paving the way for her own spinoff series and feature film. She also became the main love interest of the protagonist and basically reached Official Couple status with him by volume 13.
Mutsumi Otohime from Love Hina. Originally introduced as a one-shot character, she would later go on to become the tritagonist and the one responsible for Keitaro and Naru's Childhood Marriage Promise.
Fate Testarossa. Originally The Dragon of the first series, her interplay with Nanoha after they joined forces proved so popular, the two of them were made equal partners starting from season two, and she is essentially a co-protagonist from then on.
Nanoha herself was originally a very minor character from Triangle Heart 3: Sweet Songs Forever. She proved popular enough to get her own game, and soon afterwards - a Spin-Off show. The original concept of the show was a straight up Magical Girl series until somebody in the staff commented about her design resemblance to a Gundam. The creators took the idea and ran with it, packing the show to the brim with Magitek, tense battles that wouldn't look out of place if mages were substituted with Humongous Mecha, and, as the seasons progressed, an increasing number of Military Science Fiction and Space Opera elements. And for Nanoha herself, she is now one of the most iconic and widely recognizable Magical Girls, and by a large margin the most badass. Very few people realize that she was originally a supporting character in another series that they most likely never even heard about.
Made in Abyss: Nanachi the snarkygenderlessrabbit-person was introduced as something of a diversion when the manga's popularity was waning. Their tragic backstory and general quirkiness not only made them a big hit with the fans, but also revived sales of the manga. When the anime adaptation came out, Nanachi got three official figurines before either of the original protagonists got one.
Kumagawa Misogi is a truly outstanding example of this. Introduced as The Dreaded several chapters before his appearance as the second big bad, he then proceeds to be essentially the biggest, most destructively psychopathic troll the series had seen up to that point. However, through a combination of interesting character traits and fourth wall breaking humor he rocketed to the top of the second character poll, beating out the second place character (Kurokami Medaka, the main character) by several times the amount votes. His pinup in the poll results has him crying tears of joy at finally winning (and, probably, achieving his wish to see all the female characters in naked aprons). He's even getting his own spin-off!
Naze Youka also qualifies to a lesser extent. Originally just a member of the Class 13, once it was revealed she was the older sister to the titular character, her significance continued to increase, as well as her popularity. She's now Vice-President of the Student Council.
Plenty of Class 1-A students have become breakout characters, such as Eijiro Kirishima, Tsuyu Asui (see below), Denki Kaminari, Hanta Sero, and prety much the female ensemble of the class.
Tsuyu Asui immediately won over fans because of her cute looks, her blunt personality, and her Big Damn Heroes moment during the USJ Arc. Her popularity gave her a bonus chapter of the manga going into her backstory, gave her some Ship Tease with Deku in the first OVA, and got her a focus episode in the anime's second season, showcasing her internship that was only mentioned in the manga.
Hitoshi Shinso, a character who only played a small role as Midoriya's first opponent during the Sports Festival, became very popular thanks to his cool, highly useful Quirk, sympathetic backstory and motives, and his Creepy Good appeal. He placed twelfth and fourteenth in the first and second popularity poll, respectively, despite the fact he's only made a cameo or two since the Sports Festival. Word of God has hinted Shinso will be back in future updates, with a major part to play.
Hinata's popularity was so great that she got a ton of focus in the anime, both canon and filler, and became increasingly important as the manga neared its end. She's also Naruto's preferred love interest, her popularity exceeding Sakura's and making her the most popular female character in the entire franchise. All of it culminated in her getting promoted to main character and Naruto's main love interest in The Last: Naruto the Movie, the Grand Finale to the original Naruto manga.
Kaworu Nagisa. In the original anime, he only appears for one episode, and is then killed off by Shinji, however, his heartfelt relationship with Shinji (which to this day has a hold in both Yaoi Fangirls and LGBT Fanbase) which is arguably the healthiest in the Dysfunction Junction of the show, his design, and personality as a charming yet otherworldly boy made him a massive fan-favorite character. Subsequently, he would become a staple of the series, with him becoming a much more major character and getting focus on the movies and side-material of the franchise like video games, as well as getting plenty of merchandise.
Chopper. Most likely due to him being the most marketable character. (So much that some believe 4kids skipped arcs just to get to Chopper so they could rake in the cash.) What really brought him out was the Chopperman bits. So much so that he now has his own spinoff manga series! He's a relatively mild example, as he was intended to be one of the (currently) 10 main characters from the start. But the author probably didn't expect him to become that iconic. And the irony is that in-universe, he is merely thought of as the Straw Hat Crew's pet, only getting a bounty after Enies Lobby of 50 berries, later raised to an equally unimpressive 100 berries, highlighting how unimportant the Marines consider him.note For comparison, all other bounties are in the millions or higher If only they knew...
Besides Chopper there's also Zoro and Sanji the two most popular and strongest characters after Luffy, the former has his own movie and the latter was even voted fourth most popular character in the first character poll, despite being just only introduced and shot up to third soon after. Zoro and Sanji were both popular enough respectively to have one-shot manga spin-offs, Sanji getting a manga prequel by Yūto Tsukuda and Shun Saeki of Shokugeki no Soma fame and Zoro getting a manga recreation of his fight with Mihawk drawn by Boichi.
Portgas D. Ace, Luffy's older brother has disproportionately large fanbase compared to how little actual screentime he has in the main story. He was popular enough from the outset that the Alabasta anime expanded his role and kept him around for longer and by the time next appearances he never failed to make it to the top ten favorite characters. Despite being long since dead after the Marineford arc and having Sabo inherit his Playing with Fire powers, Ace still somehow made it to fifth place in the seventh character poll. Oda recognizing Ace's popularity has released a prequel novel series with Ace as the protagonist.
The bizarre and funny Wholesome Crossdresser Bentham (aka Mr. 2, Bon Clay) was a big hit for the show, earning him a major supporting role in the Impel Down arc and being spared from his Bolivian Army Ending. His voice actor was also such a big hit, Franky was specifically created so they could keep using his voice.
Boa Hancock. One of the Shichibukai and Amazon Lily's empress, she went from antagonist to one of the most loved characters of the franchise, mainly because appearance and her comical, hopeless, and totally over the top crush on Monkey D. Luffy, the protagonist. Notably Hancock appears in both J-Stars Victory VS and Jump Force despite not being a main female character like Nami or Robin.
Trafalgar Law, the Surgeon of Death, had a meteoric rise to popularity. When he was first introduced in Sabaody, he was liked well enough for his design, personality, and uniqueDevilFruitpowers, which earned him the tenth spot on the character polls. Then he was reintroduced in the Time Skip during the Punk Hazard arc, given greater focus, and with his powers and backstory being explored, earning him greater love from the fanbase. By the time of fifth character poll in Dressrosa, Law had achieved the unthinkable and superseded Zoro as second most popular character after Luffy, meaning he is without a doubt the Breakout Character of the series.
Osu! Karate Club: Anti-Hero Yoshiyuki Takagi from the manga was originally the mentor of the original main character, Tadashi Matsushita. Takagi became so popular with readers, that the author decided to make him the main character, reducing Matsushita to a supporting role.
The Gold Saints, from Saint Seiya, serve primarily as the ultimate obstacles for the heroes in the Twelve Houses Arc but, due to their popularity, their roles started to become more important as time passed by and more prequels where created to the point that they have perhaps surpassed the heroes in terms of screen-time (anime and manga combined) and became the protagonists of their own manga in Episode G (and Lost Canvas to some extent).
Yun of Simoun. Originally tripping all of the Sacrificial Lamb flags (not in the OP when the character that's introduced alongside her is, portrayed as a prideful, somewhat antisocial fool who refuses to listen to the wisdom of others, etc.), creators reacted to her unexpected popularity by giving her one of the most important roles in the story.
Zelgadis the chimera and Amelia the princess were protagonist duo Gourry and Lina's allies for a couple of novels and were eventually replaced. When the anime began branching off from the novels, chimera and princess had proven popular enough to become as major characters and as integral to the story as Lina and Gourry. All adaptations of manga and games have followed suit with this. The replacements, on the other hand, are virtually unknown.
Xellos the demonic priest is also this combined with Ensemble Dark Horse; he only appears in five books (cameoing in the last one); like Zelgadis and Amelia above, he became more integral as the franchise evolved.
In 2006 Tsuji Santa drew an illustration of a busty pink-haired girl wearing headphones and sporting a guitar, that was just a poster to promote Nitro + Music Festival, nothing more. That poster grew to be immensely popular and Super Sonico was born, Nitro + saw marketing potential in her and started to invest in the character, figures, posters, music, manga, video games and anime were made, Super Sonico became one of Nitro + greatest brands, making her the official mascot for their music festivals, and made Tsuji Santa a more renowned artist who went on to create more characters in the same vein as Super Sonico.
The To Love-Ru sequel, To Love Ru Darkness, took the secondary character and fan favorite Golden Darkness and promoted her to the co-protagonist position, alongside with Momo (character introduced more later in the first series) the steal the main heroine role to her big sister Lala.
Lum in Urusei Yatsura was supposed to be an One-Shot Character, but fans (and Takahashi's editor) loved her so she returned in the third chapter and became a Deuteragonist, love interest, and poster girl for the series. She is often believed to be the protagonist of the series due to her iconic status. In the Real Life she is become one of the most beloved and representative characters in the manga world.
A non-character example: the Duel Monsters card game, which was originally meant as just one of many games played throughout the series, but eventually became so popular that the series was given a Retool to make it the only game that mattered- even the few games played that weren't Duel Monsters were still about battling monsters. This carried over to the sequelseries, where there's barely a hint of any other games.
For a character example, Kaiba, who was made to be a one use enemy for the Duel Monsters chapter and got to come back as a larger villain due to popularity, then as one of the most important characters after that, tied to the Pharaoh's backstory itself.
Pegasus. Despite being dead in the original manga, in the anime he was so popular that they kept him alive. He returns in several cameo appearances in GX, even getting to duel again, he's the Big Bad of the Yu-Gi-Oh! Reshef of Destruction video game, and he features in two mainstream movies. By contrast, Yami Bakura and Marik tend to get plot-irrelevant fights or cameos in video games.
The most famous card is the Dark Magician Girl. She became one of Dark Yugi's key cards, she makes appearances in all the spin-offs in some way or another, and has a lot of alternate art cards and Expies. No other card aside from the Dark Magician or Blue Eyes can make such boasts, and even then, they never got to be a playable character in some of the video games, but she did, and in some others merchants in card store chains dress as her.
Hiei from Yu Yu Hakusho was originally meant to be a one-shot character (this is clear in his first appearance), but he proved so popular with fans that he was given another appearance - and continued to prove popular enough with fans to make him a main character, complete with his own plotlines and backstory.