Luna Lovegood, pictured to the right. Originally only to have importance in Order of the Phoenix, by the end of the series she is the sixth member of the Harry PotterTrue Companions, and the only non-Gryffindor to be in it.
Luna's so popular, she managed to make her Quibbler critters a popular source of Arbitrary Skepticism jokes in the fandom, and many fans were disappointed that she never discovers a Crumple-Horned Snorkack during her time as a Magizoologist.
Albus Severus Potter. Largely because of what his initials spell, and considering that the Slytherin House is associated with snakes...
Professor McGonagall gets this as well. Originally introduced as a typical Stern Teacher, her hilarious comments during Quidditch matches, loyalty to Dumbledore and Harry, especially in the fifth and seventh books, as well as a few stunning feats of magic during the Battle of Hogwarts, she's becoming synonymous with Cool Old Lady.
The Weasley Twins, Fred and George, mainly because they are the living example of Crowning Moment of Funny (which is also very necessary, as the books get so much darker as the series progressed).
Snape, Snape,Severus Snape. It helps that he's played by Alan Rickman in the films, but even before that, he was already hugely popular among the readership. The Sadist Teacher and Red Herring suspect in the first book who seems to be trying to steal the Stone and kill Harry in the Quidditch game. When the truth turned out to be the opposite (he was trying to keep the real culprit from stealing the Stone and saved Harry's life in the Quidditch game) he became bizarrely fascinating. An outwardly nasty character who is working with the good guys, he introduced a shade of gray in what seemed at first glance to be a Black and White Morality series. With his devastatingly witty put-downs and his big black cloak, he became a Draco in Leather Pants to rival Draco, with the justification that he was seemingly a good guy. Then came the sixth book with the shocking plot twistthat everyone now knows. It says much of his popularity, that for the seventh book, Scholastic put much of it's publicity around him with its "Snape: Hero or Villain?" debates, despite his minimal appearances in that book. Those appearances didn't disappoint, revealing a tragic backstory that justified much (but not all) of his nastiness, making him probably the biggest Love It or Hate It character in the series.
Both Remus Lupin and Sirius Black are very popular characters amongst the fans, placing 6th and 5th respectively on this list of the greatest Harry Potter characters, behind only the Golden Trio and Snape.
Antonin Dolohov has his share of fans. Possibly due to being one of the more competent Death Eaters and almost always winning the duels he participates in.
The fans are so crazy even characters who barely get mentioned at are, such as Daphne Greengrass, the Patil twins and Susan Bones, or not at all, are at times more popular then established characters over the time frame of several books, such as the Gryffindor Chasers, Cho Chang, or Justin Finch-Fletchey.
Tonks. Fans love her
Tobias and Ax from the Animorphs series. They were only given one book apiece for each ten book cycle, while the other four Animorphs got two. This was done because Scholastic didn't think these two characters would be as popular as the main cast. Later, as the series was nearing its end, Scholastic finally realized how wrong they'd been about that and mixed up the release order so Tobias and Ax would get more books.
Reepicheep is also incredibly popular, possibly due to his swashbuckling style.
R.A. Salvatore originally meant for his popular dark elf character Drizzt Do'Urden to be a side-character for Wulfgar, Drizzt's barbarian pupil, in the first novel they appeared in; he claims to have come up with him on the spot when his agent asked for a sidekick for Wulfgar. Naturally, at this point, they're collectively known as the Drizzt books. This is one of the unusual cases where transitioning the Darkhorse into the main hero's role actually worked.
According to the introduction to one of the books, this conversion happened early in the writing process (basically, page one).
Murtagh from Eragon, who is often seen as cooler than the eponymous hero, and a lot less whiny about it.
The Artful Dodger in Oliver Twist is probably the best remembered character of the novel in modern times, if not the most celebrated character in Dickens' whole body of work.
Billy Bunter began life as a minor character in the Greyfriars school stories. Comically greedy, snobbish, dishonest, inept, self-centred, lazy, stupid, mean, cowardly and always, always on the scrounge, he provided the perfect foil for his upright and honest classmates and became so popular that he eventually took on the title role for the series.
However this may have been Milton's intention. He wanted to show how seductive evil can be, Satan possibly being an Oliver Cromwell type figure, though reading the book carefully shows deliberate Motive Decay from Satan.
It's certainly the case in Paradise Lost. Adam is nominally the hero, but he's far less interesting and spends a lot of time simply chatting with Eve and the archangels. By contrast, Satan gets a character arc and complex motivations, and ironically seems more "human". It attracted numerous criticisms of Milton at the time.
Bronn is virtually an Ascended Extra, starting off as one of a pair of sellswords who join a large crew of Red Shirts to escort Tyrion to the Eyrie. By the time his partner and most of the redshirts have died, Bronn has become Tyrion's badass bodyguard. When he's not kicking ass, he's usually sharing witty banter with Tyrion, making him prime fodder for fandom.
Podrick Payne, Tyrion's squire, is widely loved in the fandom for his Adorkable shyness and the generally stoic way in which he bears the various indignities of being a minor character in this series. His Crouching Moron, Hidden Badass tendencies also help, with his two best moments in the series so far being pushing Ser Mandon Moore into the Blackwater to save Tyrion's life and distracting the Bloody Mummers so Brienne only has to fight one at the time.
One of Ser Jaime Lannister's squires, Josymn "Peck" Peckledon is also fondly regarded by some fans as a darker counterpart to Pod, namely because, whilst Pod is a hiddenBad Ass, Peck is just a straight up Bad Ass. His best exploit to date was at the Battle of the Blackwater, when, aged fifteen, he killed two knights, crippled a third and captured two more.
Nearly every minor Lannister, but most particularly Ser Daven, Ser Kevan and Lady Genna, is regarded with affection throughout the fandom.
Littlefinger is arguably not a darkhorse given his very active role in engineering much of the series's plot, but he has developed quite a large fanbase who want him to succeed, despite arguably being a villain.
Oberyn Martell, the Red Viper of Dorne, is such a colorful and interesting character that he has developed an extremely large following despite his very limited time in the series.
Averted with Darkstar, an admitted attempt by Martin to write a new ensemble darkhorse, simulating Oberyn. Most fans didn't bite, due to his overly forced Draco in Leather Pants pretensions and bungled attempt to assassinate a likable little girl.
Lady Olenna, Queen Margaery's grandmother. Plotted Joffrey's death with Littlefinger, wanted to help Sansa get to a safe place until she could be sent North to her mother and brother, and master chess master who gets under Cersei's skin so much.
Wyman Manderly, the Lord of White Harbor, was essentially a background character whenever he appeared in the first four books. However, in the fifth book He has three members of the treacherous House Frey baked into pies and served to their kinsmen at a wedding. This action undoubtedly elevated him to Darkhorse status.
Also from Dragonlance, Kang, Slith and the Doom Brigade. Their unexpected popularity resulted in an unplanned short story and many cameo appearances in other books.
Terry Pratchett, the author of the Discworld series, claims that this is the greatest danger when you create a throwaway character. The best example is Death, whom he only created as a one joke character, but liked so much that he gave him multiple additional appearances in the first two books. Samuel Vimes and Granny Weatherwax also started out as support characters.
And then Death appeared in every book, got three books of his own and a daughter, son-in-law and grand-daughter. With that, it's hard to argue that he isn't the Disc's main character now.
And Detritus, who started as a "splatter" and became Sergeant and head of the Watch's training academy, married to Ruby, and "adopted" Brick.
Pratchett began writing "Guards, Guards" intending for Carrot to be the main character. Then he slowly got more interested in a side character he'd only created to provide a point of view in Ankh-Morpork until Carrot showed up, and now Samuel Vimes is easily one of the series' most popular characters. It's gotten to the point where Pratchett has had difficulty writing books set in Ankh-Morpork without turning them into Vimes stories.
The Riftwar Cycle spans over thirty books. One of them - a novelisation of a video game set in the world, no less - features Gorath, a dark elf chieftain, who defects to the side of the humans to prevent another war his people are trying to start that he knows would be too costly for them. Gorath is easily one of the most complex and intriguing characters in the entire cycle, not even counting being cool as hell - unlike some other dark elf renegades *coughDrizztcough*, he is dignified and stoic, despite having a backstory that would justify anything from Wangst to a complete insanity breakdown. Even though he appears alongside such fan favourites and scene-stealing characters as Pug and Jimmy the Hand, fans and critics alike praise him and wish they could have seen more of him.
Twilight also has its fair share of Ensemble Darkhorses.
Jacob Black was originally meant to be a one-shot character who would introduce Bella to the myths of the "cold ones" (vampires), but Stephanie Meyer and the readers ended up enjoying him so much that he became very important to the overall plotline of the next three books and Bella's best friend and second love.
James was simply a member of the Wacky Wayside Tribe of nomadic vampires introduced in the first book whose only purpose in life was to hunt, kill and drink good blood, namely Bella's. He's described as being unremarkable in appearance, average even by human standards. But he became inexplicably popular with the fans when he was revealed to have a connection with Alice, and his lack of an established past made him a point of interest for theorists. It also did not help matters that Cam Gigandet, the actor who played him in The Film of the Book, was very admittedly attractive, and when asked to come up with his own interpretation of the character, said that James was really a broken hollow shell of a person on the inside, coming damn close to making James The Woobie as well.
Leah Clearwater earned this title for her Deadpan Snarker tendencies and the fact that she unflinchingly and unapologetically would call out the other characters whenever they acted like idiots. She also had many of the makings of The Woobie as well, having lost her father to a heart attack and her boyfriend Sam leaving her for her cousin Emily ever since becoming one of the wolves, and yet having everyone shun her and treat her like a bitch, not caring at all about her heartbreak (something that thankfully changed when Jacob left the pack and was able to get to know Leah without any influence from the others' prejudice.)
Leah's little brother Seth Clearwater has a small part to play in Eclipse, and picked up a massive following for his adorable snark, bravery, and almost naive affableness. Come Breaking Dawn, he had a lot more action and some of the best lines in the book.
Many of the Volturi became very popular amongst the fans as well, despite having not many lines or characters.
And after Breaking Dawn, Nahuel, a Dhampyr brought in by Alice to testify against the Volturi and convince them that Renesmee Cullen was not a threat to the vampires' existence, who was also a Dhampyr herself gained quite a fandom as well. His only real lines were his testimonials, but more of his character was revealed by Edward's mind-reading, making him a bit of a woobie as well. In Fan Fic, he's usually paired up with fellow darkhorse Leah. A bit of a Crack Pairing, yes, but some can't help but find the idea of it very inexplicably cute.
And Angela is liked even by Anti-fans, due to the fact she's a genuinely sweet girl, but due to being a Muggle after Bella's a vampire we never see her again. A lot of antis like the humans (Mike, Jessica, etc) because they are looked down upon by Bella and Meyer for being better characters.
There is also a need to mention Tyler (and his van.)
Charlie Swan is another one who's quite popular even among the haters, who often call out Bella for the hell she puts her father through.
The character Rupert Psmith from Wodehouse's Psmith series started out as a comedic sidekick to the titular character of the first book he appeared in, Mike Jackson. However Psmith's character became so popular that the roles have been reversed in every following publication which now all bore Psmith's name and even the original first book's title was changed from "Mike" to "Enter Psmith" and "Mike and Psmith".
The anonymous undead penguin from Langley's Ark has a disproportionately large fan following, which was solidified in a Q&A session with the cast. Somewhere down the line, it became the Series Mascot.
Langley: I would just like to add at this point that my name is even part of the title and the penguin has gotten more questions than me.
In the Gaunt's Ghosts series Major Rawne started out as a relatively minor, two dimensional character. He is now one of the most complex and well loved characters of the series, to the point where the author Dan Abnett admitted that the grumpy Major was his favourite character, ahead of the titular Guant.
Charlie Parker is the main character of a detective series that puts Irish thriller writer John Connolly on the literary map, but fans loved Parker's gay assassins sidekicks Angel and Louis so much that Connolly finally wrote a novel The Reapers in which the two has the starring role and Charlie Parker remains in the sidelines until right before the end of the novel.
Mr. Micawber from David Copperfield with a lot of thanks to WC Fields' unforgettable 1935 film portrayal.
Within the Sweet Valley fandom, Lila Fowler (Jessica's primary snobbish friend) is wildly popular - often more so than the Wakefield twins themselves (each of who have more than their fair share of detractors, for different reasons).
The sheer amount of characters in the whole Middle-Earth universe allows a fair share of this. Especially characters in The Silmarillion which wasn't originally supposed to be published. Special note goes to the other three Istari who are this even though two of them literally do not appear. A lot of the Vala also qualify, given that they appear just in the beginning.
Tom Bombadil's exclusion from the movies caused a long-lasting storm of fan rage. On the other hand, many other fans consider him, and the two-and-a-half chapters devoted to him, to be utterly pointless, or at the very least, utterly unfilmable.
Erestor, especially in slashfanfics. In the books, he's just Elrond's chief counsellor, who appears at the Council of Elrond but does not make any significant contribution (he suggests the Ring be given to Tom Bombadil, and doesn't think trying to destroy the Ring is a good idea.) In fanfiction, however, he somehow tends to become the most beautiful, smart, witty Elf in Middle-earth and gets slashed with just about everyone.
Glorfindel from The Lord of the Rings was named after another Glorindel: one who faced a Balrog in single combat and even manages to defeat it by knocking it off a cliff. Gandalf, apparently, took notes.
Except Tolkien has stated that those two Glorfindels are one and the same. Elves, unlike Men, were bound to the world so when they "died" they would sometimes be allowed to leave the halls of Mandos(the Valar in charge of the dead Elves) and reincarnate. This was less true reincarnation, though, and more along the lines of picking up where he left off. That's right, the Glorfindel from the Third Age is the same one from the First. Battle For Middle Earth II showed us just how badass Glorfindel is.
Nerdanel and her son Maglor are disproportionately popular compared to the number of times they're actually mentioned.
Elladan and Elrohir are also very popular among the fans despite the fact that they were rather minor characters. Rather ironically, they did not make it to the movie even though they actually appeared more than their younger sister, Arwen.
The Variags of Khand as a race in general. Despite only being mentioned in a few sentences and never being described in any aspect, there's an immense amount of speculation regarding the Variags on Tolkien fan sites.
Sugar and Ice Personality werewolf Dominil was a supporting character whose character arc was completed when she knifed Big Bad Sarapen in the guts in the first Lonely Werewolf Girl book, by the time the second came around she was promoted to main cast member with a new character arc.
The Thrawn Trilogy introduced quite a few. Pellaeon is perhaps the most notable, with his excellent character growth making him immensely popular among fans, to the point that he eventually became the person to end the Galactic Civil War. Thrawn himself, despite only appearing in a scant few books, is a borderline Memetic Badass, and regarded by many as the face of the Expanded Universe.
Sherlock Holmes has Irene Adler and Breakout Villain Professor Moriarty. Irene Adler is in only one story and barely seen in person throughout, but she's the only person ever really seen to beat Holmes and is one of very few female characters in the canon, so she gets saddled with 'love interest' a lot. Moriarty appears in one story and gets mentioned in three, but him being anything but the enemy of Holmes has become unthinkable.
And then there's Mycroft Holmes, Sherlock's Brilliant, but Lazy older brother, who only appears properly in two stories, has a non-speaking role in another, and is mentioned only once in another story, but he has a surprisingly large fanbase.
In The Hunger Games trilogy we have Finnick - he was only a minor character in Catching Fire and more minor in Mockingjay but he became extremely popular for his kindness, strength, sense of humor, and dedication.
Katniss might be the protagonist of the story, but in the Games depicted in the first book the Tribute who won the fan's hearts the most was Rue. She had all of Katniss's sister Prim's finer qualities while lacking the Shrinking Violet, being a Plucky Girl-in-training despite her age and small size, and her bond with Katniss was extremely sweet. There's also Cinna, who makes fashion designing and makeovers awesome, and quickly won both readers and Katniss herself over thanks to his approachability and compassionate nature.
Foxface also gets a lot of love thanks to her cleverness, despite only appearing in one book, not having any speaking lines, and not having an actual name.
Thanks to the One-Scene Wonder nature of the film, Thresh and Clove have also become this.
Johanna Mason also has quite the fan follwing.
Nico di freaking Angelo from Percy Jackson and the Olympians. He goes from this bratty little halfpint obsessed with a cardgame and always asking a million questions in Book 3, to something of an enemy in Book 4 because he blamed Percy for the death of his sister, to pulling the biggest Big Damn Heroes moment of the entire series in Book 5.
Artemis and Apollo. Arguably the least featured Olympians, and they are the most popular on Fanfiction.net. Is it the fact that you have the 12 year old badass or the humor of Apollo's Haikus of terror?
Mocking Octavian is rising to become Percy Jackson's mocking Umbridge style game
Leo, the wise-cracking sidekick with Hidden Depths in The Heroes of Olympus. While Jason & Piper (the in-universe heroes) had a murky reception, Leo instantly became a fan-favourite and universally adored. This status only increased in Mark of Athena, with his tragic past which is more brutal than most of the other heroes put together, status as the 'Seventh Wheel' among the happy couples and that despite this, he never stops joking the whole time.
Pick a character or kingdom. While there are mainly Wuists, Shuists, and Weiists, the three main kingdoms, every minor force gets a following as well. Minor characters as well.
Special mention has to go to Mi Heng, who appears in one chapter but is still one of the most popular characters. Every single line he has is a vicious insult towards whoever he's talking to, with no thought toward his personal safety even as he's about to be executed.
Fitz Kreiner, from the Eighth Doctor Adventures', doesn't seem to have been ever intended as a one-shot character, but looks like one for most of his first appearance, and was obviously initially conceived as the kind of character who could be Put on a Bus at a moment's notice by making him settle down with the Girl of the Week. Now he's either the second or third longest-running companion. He appeared in about fifty-five novels and one Big Finish Doctor Who audio play. Numerous fans have admitted to liking him better than the Doctor, and he's one of the few companions who seem to be disliked by only two or three people of a mind to complain about it on the Internet. Indeed, almost everyone thinks he's pretty groovy. It's probably got a lot to do with his Ho Yay with the Doctor, but there are tons of other reasons.
Scourge, a villain who only appeared in one book but gained lots and lots of fans and sometimes a Draco in Leather Pants status, simply because he's Bad Ass ( He killed Tigerstar with one hit! He took away all his nine lives with one swipe of his paw! He got to be so popular that the authors made a whole manga book about him, detailing his past and his Start of Darkness as well as giving him a Freudian Excuse, which doesn't excuse him for his evilness but does give you a reason to feel sorry for him.
Flametail, a Breakout Character who is the son of Tawnypelt, a Darkhorse in her own right, counts for being a Combat Medic with complete faith in StarClan.
Most leaders and deputies in Warrior Cats are Darkhorses. Case in point: Mistystar, Stonefur, Ashfoot, Tallstar, Deadfoot and Leopardstar. Crookedstar counts too, being a minor character who died in Book Five, yet placing second in the Ultimate Leader Election.
Snowkit, a very minor character killed off in A Dangerous Path has a massive fanbase because of his woobieism. He's a deaf kit who was carried off by a hawk.
Snowtuft and Shredtail, who died before their first appearance, mostly because Evil Is Cool.
Hawkfrost is quite a Darkhorse. Despite only being Tigerstar's dragon and serving a mere lackey role in the arcs after The New Prophecy he remains one of the most popular villains and is directly featured in the "games" on Warrior's Wish.
Hazeltail, a background character who has done exactly nothing in the series is very popular on the Warriors Official Forum and ranks very high on all the polls for the fanbase's preferred new ThunderClan leader.
Ravenpaw. He was part of Firestar's Power Trio in the first book, then left and has only played a minor role since then. Despite this, he was popular enough to get his own manga series and have hoards of fangirls wishing for his return.
Sorreltail is one of the more popular characters and is possibly the most popular choice for ThunderClan's new leader, despite only playing a small role in The New Prophecy and being even less important after that.
Harrykit of SkyClan has earned many fans. He's even become a Memetic Badass, with people claiming that he's a wizard and his warrior name will be Harrypotter.
Brightheart. She's quite possibly the only character in Warrior Cats, which is practically defined by it's Broken Base, who has no haters.
Foxleap. He serves as a comic relief character in Power of Three and only ever plays an important role in the fourth book of Omem of the Stars, but he has a large fanbase and all sorts of speculation over if he's the fourth.
The clan founders, Thunder, Wind, River, Shadow and Sky. Even though they have only one scene in the main series and appear very little in the Expanded Universe, they are extremely popular and all of them have achieved Memetic Badass status and many fanfics devoted to them. In fact, they seem to have attained Breakout Character status as well, seeing as the fifth series will focus on them.
Antpelt has become a very popular character, despite only appearing in three books and having his return be impossible. His fanbase is so large that it even managed to (The Forgotten Warrior spoilers) make the incredibly popular Ivypool become a Scrappy temporarily when she killed him.
Happykit. How minor is this character? Their sole appearance is in The Last Hope as a dead ShadowClan kit that Pinenose is crying over. Even the name is fanon! Despite this, Happykit has received quite a few fanfics, and is legendary among the fandom.
Silver Frost, a cool elder from the Tribe Prime, seems to be the most popular character to appear in the preview chapters of Dawn of the Clans.
Now that Dawn of the Clans: The Sun Trail is out, the most popular character is easily Tall Shadow, the snarky, intelligent she-cat who may be ShadowClan's founder.
In Young Wizards, Kit's sister Carmela doesn't even show up until the fifth book, and then it's only as a slightly dippy otaku big sister. Now she's a pretty major supporting character and kind of a Genius Ditz with languages to boot.
Dairine Callahan, the Nita's little sister, is seen by some as this and by others as The Wesley.
Hurin, the Sniffer from Shienar, plays a role in book 2, The Great Hunt, of The Wheel of Time, although his main purpose is to provide Perrin with an opportunity to take his place where necessary. Part way into book 3, he leaves to return to Shienar, and is not seen again until book 12, The Gathering Storm, practically as a cameo. Despite this, he is a highly regarded character, and prior to the release of The Gathering Storm, he was perhaps the character that people most wanted to see return.
PrinceGarrid from Tales of the Frog Princess. The audiobooks helped a lot. Must be the Romanian accent.
The Pickwick Papers: Samuel Weller was introduced in a minor supporting role as the main character's cockney valet partway through the serial, but quickly developed a massive following that almost single-handedly kick-started Charles Dickens' career.
Alice in Wonderland: The Mad Hatter. Not in the books themselves, or any of the original movies. But in any more recent adaptation, the Mad Hatter is likely to get a large amount of screen time.
Pride and Prejudice: Even those that groan at reading the book, nay even some haters, love Mr. Bennet and his snark.
Tony Foster from Tanya Huff's Blood Books. Originally just an informant to the protagonist Vicki Nelson, his role gradually grows until he becomes Henry's live-in boyfriend. Then he moves on to his own series where Vicki is almost entirely absent and Henry assumes the role of sidekick (although he would never admit it).