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Malon has never played a prominent role in the series, and discounting the remake of Ocarina of Time she hasn't made an appearance in years. She's still one of the most famous females of the series aside from Zelda, and a popular target for shipping.
And if he weren't already enough of a Darkhorse, you can gain the power to summon his ghost in Skyrim.
Sheogorath, the Daedric Prince of Madness is incredibly popular, due to the fact that being Crazy Awesome is his entire job.
On a similar note (speaking of Crazy Awesome), there's a portion of the fanbase that really likes Pelinal Whitestrake for the same reason.
Lydia from Skyrim quickly gained this status in the first few days of launch. One of the many companion characters who can be gained early in the campaign, she stands out for many reasons, among them the facts that she's well-armed, attractive, and sarcastic—as well as given to you as a housecarl as part of the main quest.
Serana from the Dawnguard expansion, due to the depth and dimensions given to her character, as well as the subtle Ship Tease between her and the Dragonborn. Indeed, the Dragonborn takes the role of Supporting Protagonist in Dawnguard, which is ultimately her tale.
Jarl Balgruuf is very probably the most popular of the Jarls due to the fact that when you have to capture a live dragon, he decides to grab an axe and get stuck in personally.
Dog was so beloved by the fans that Valve ensured he would be the first thing the player sees at the beginning of Episode One, and was reintroduced in Episode Two by fighting a Strider and tearing out its goddamn brain.
FatherGrigori, who appeared in one level and was never even mentioned again, yet is still remembered as one of the best parts of the game.
A large amount of fans of the original storyline of Half-Life 2 like Animal, who would be a rebellious footsoldier and he is noted for being frantic and nervous. He would only be seen briefly before getting killed by a sniper.
Adrian Shephard, player character of the Opposing Force expansion, had no affect on the overall storyline and isn't mentioned anywhere else in the series, but many years after his appearance fans still clamour for him to return to the series in some way.
One of the most bizarre Darkhorse characters ever is the Weighted Companion Cube from Portal. It's literally just an inanimate box. This is arguably intentional, as it was a trick by the developer's to make sure you kept that Cube with you as your friend; when people didn't care about it, they'd leave it behind and not realize they needed it to complete puzzles.
The Space Core from the end of Portal 2 joins the Companion Cube amongst the darkhorses of the series.
Tachibana Ukyo from Samurai Shodown, a badass swordsman afflicted with tuberculosis, was intended for death early on in the series. However, due to popularity among fans, he was not killed off and has appeared throughout the series. Or rather, the latter Samurai Shodown game stories is always set in a timeline where they can always include Ukyo (that one game that didn't have him turned out to be a flop). Also further addressing to the trope, come the second game, Ukyo takes a huge step down from story relevance thanks to being ousted as the true rival of Haohmaru by Genjuro, and each game diminishes his importance. He's still a fan favorite either way.
Iroha seems to be another case; despite a single appearance in the series (in VI), she is popular enough to gain a spin-off game starring her.
Cham Cham is also quite popular for someone who only appears in three games (II, IV, and VI; and in IV, she was a PlayStation-exclusive character). She even has her own pachinko game.
Shiki from the Hyper Neo Geo 64 titles is quite popular as well. Even though she never made it to the main series, she was among the first characters from her subseries to make it into other SNK crossovers, such as SNK vs. Capcom: SVC Chaos and Neo Geo Battle Coliseum.
Originally the only other "chick" in the roster aside from Chun-Li, Cammy became popular enough to appear in several of the game's crossovers. Sakura, who debuted in Street Fighter Alpha 2, also became popular enough to have her own comic book, which spawned the Canon Immigrant character Karin, who appeared as her rival in Alpha 3.
Dan Hibiki, the quintessential Joke Character who first appeared in Alpha, has also become unusually popular because of his status as such.
There's also Guy, the Bushin ninja who crossed over from Final Fight, and Fei Long, one of the original Bruce Lee Clones in video games (indeed, Fei Long is the only "New Challenger" from Super Street Fighter II other than Cammy to return in the original version of Street Fighter IV). Charlie/Nash is also pretty popular, despite the fact that in his first chronological appearance, he dies.
And then he dies again. Both in Street Fighter Alpha 2, which, to be fair, was actually superseding the first game's canon, but then, more absurdly, resurrected and killed once more in Alpha 3. He might have even been brought back as "Shadow" after that, but Capcom's never really come to a conclusion on that point.
Alpha 3 had two in Karin (the aforementioned rival to Sakura) and busty masked wrestler Rainbow Mika. In an official 2013 character poll by Capcom, Karin was the surprising fan favorite among Japanese SF fans, outranking Ryu, of all characters.
Dudley of Street Fighter III fame is easily the most popular original character from his series, to the point where he was ranked 1st in an online poll held by Capcom to determine which characters should show up in Super Street Fighter IV.
Also from III is Genki Girlprincess Elena. She just barely missed being included in SSFIV. And then we have the Lee Bros., Yun and Yang, who actually did make it to the arcade version of SSFIV. Yun also has the distinction of making the most crossover appearances out of the entire SFIII cast.
From Street Fighter EX, there is one name that stands above all: SKULLOMANIA. Perhaps the campiesthomage to all things Toku, he is a walking Crowning Moment of Funny. In the poll for Street Fighter IV (the same one that Cammy won), he came in second place. Clearly, Skullo is the darkhorse among darkhorses. And that's not getting into the likes of Garuda (who's second in regards to Skullo), Pullum, Doctrine Dark, Hokuto, Kairi, Cracker Jack (who was probably the original Dudley), Darun, Blair, Allen...
And speaking of IV, the two female additions, no-nonsense CIA agent (and mother of one) Crimson Viper (vanilla SFIV) and the deliciously insane and evil Taekwondoka Juri (Super), have pretty much overshadowed the other newcomers, to the point that Viper is the fourth SF rep in Marvel vs. Capcom 3 (alongside Ryu, Chun-Li, and Akuma). Would you believe it that Abel was supposed to be the focal point of IV? Didn't think so.
Officially, the main protagonist of Darkstalkers is the vampire Demetri Maximoff. His spotlight, however, is regularly taken by other members of the cast, chief amongst them his rival Morrigan Aensland, who has appeared in every Capcom vs. Whatever crossover game since the original Marvel vs. Capcom. While nowhere near Morrigan's level of popularity, other characters such as Felicia, Hsien-Ko, Lord Raptor, and (especially in America) Jon Talbain have strong fan followings.
Jack Krauser from Resident Evil 4 was such a popular villain that he reappears in Resident Evil: The Darkside Chronicles, where he receives a more detailed backstory, and reappeared in The Mercenaries 3D. Not only that, but he's even a favorite among the creators themselves.
The Memetic Mutation of the first game's legendarily bad voice acting led to throwaway character Barry Burton becoming a playable character in Resident Evil 5 and its "Mercenaries: Reunion" mode. Note that the rest of the Reunion cast consists of the main characters, The Dragon, and the helicopter pilot from RE5 itself, as well as long-time recurring character Rebecca Chambers; Barry's completely-out-of-the-blue appearance is the Crowning Moment of Awesome for many fans who enjoyed mocking his deadpan delivery of his lines. Capcom understands this to the point where his Narm-tastic "I have THIS!" line about his revolver has carried over to RE5.
HUNK appeared in a flashback cutscene in Resident Evil 2 in which his entire team is thrashed. However, he wears a gas mask and had a minigame, making him popular with many fans.
Manuela from The Darkside Chronicles seems to be heading in this direction despite canon suggesting that she'll only be a one-shot character (she survives the events of the game and is taken into the custody of the U.S. government). That lovely singing voice of hers is probably why. She gets bonus points for actually becoming one with the T-Veronica virus to no ill-effect (something Alexia Ashford couldn't do) and then using saidpowers to help out Leon and Krauser during the final battle.
There is also Kunimitsu (backstabbing former member of Yoshi's Manji Party) and Jun Kazama (one-time partner of Kazuya and Jin's Missing Mom). When the Time Skip occurred to set up the plot of 3, these two ladies were the only members of the 2 cast to not reappear by the time of 5: Dark Resurrection (not counting the Killed Off for Real King I and Armor King I), causing an inordinate amount of ruckus from the fans trying to get them back on the roster in subsequent games. This seems to have worked in their favor, as Jun is a playable character in Tekken Tag Tournament 2. Kuni joined the fray as a DLC character for the console port.
Aside of that there's Emilie de "Lili" Rochefort. She's introduced in the expansion of Tekken 5 (Dark Resurrection) and seems to have no importance storywise so far, but she proved really popular due to her rich girl design, young age and easy-to-use character without being much of a button masher, enough that she appeared in the trailer of Tekken 6 (as the only character shown besides Jin and Hwoarang), and then appears in the crossover game Queen's Gate: Spiral Chaos as the only Tekken representative. Oh, and a magazine also put her on the cover while wearing a bikini. Remember, folks. This is after she is introduced in just two games.
There is also Eddy Gordo, a character that was formerly widely hated for being formerly a character that was easy to button mash with. However, the fact that Christie initially replaced him, along with button mashing turning into a much less effective method helped boost up his popularity to the point where he is a heavily wanted character in the official Tekken X Street Fighter poll. Other Ensemble Darkhorses includes Hwoarang and Ling Xiaoyu.
All of the characters of Skullgirls have fan followings, but special mention goes to Painwheel: even though she is not the most visually attractive character, her backstory and deadly moveset, along with stellar voice work by Danielle McRae, helped her become a firm fan favorite.
Kai Kitamura seemed like a new character simply there to fill in the party until more were available in Original Generation, but once it set into players that he can stop a rampaging Super Robot with little more than a Mook-level Gespenst using manual controls, WITHOUT preset commands, Memetic Badassery ensued. These days, it's hard to see Kai as anything but the epitome of Badass Normal, who turn a simple Mecha-Mook into a weapon of mass destruction.
Also in the department of hamming their way to darkhorse popularity is Disgaea's Captain Gordon, Defender of Earth! In a game with 14 "episodes", he's not even introduced until the preview for episode 9 (which is one of only two episode previews that's actually accurate), and doesn't join the party until you beat him as the boss of that chapter. He then proceeds to utterly dominate the storyline for the next four episodes before finally taking a backseat to Laharl and Flonne for the final episode... except even then, he manages to dominate, because that's when Kurtis returns from the dead. And then there's the alternative "human world" ending... normally, when a character hijacks the plot like that, they'd be hated, yet Captain Gordon, Defender of Earth is easily among the most popular characters in the game. Again—only playable for the final five episodes, or about 35.7% of the story.
However, this seems to be more of a case of Americans LoveCaptain Gordon, Defender of Earth, considering he is a parody of their nation's hero archetype. In various image sites (like Danbooru), mostly dominated with Japanese artists, Captain Gordon, Defender of Earth has very minimum amount of fanarts.
Another example is the Dark Adonis, Vyers Mid-Boss, the recurring enemy that is eventually battled five times. Also shows up a couple of times without fighting you. Granted, he does turn out to have a lot more plot significance than his apparent comic relief role would imply, but it's likely that the comic relief bits are what make him so popular. Well, that and the faceand the perpetually barewell-defined chest.
Asagi and female archers are quite popular as well. The former was 5th in a Japanese NIS character popularity poll and the latter was 11th. Most of Asagi's popularity comes from the fact that she's been largely unsuccessful in her quest for main character status (only appearing as a Secret Character in several Disgaea-related games; NIS has seemed to turn this into a Running Gag for her).
And if there's another boom (such as Vesperia), he may step aside from the first place (as Yuri Lowell beat him), but WILL always tail behind as second place, as if ready to take over the spot again when the boom died out.
But even Vesperia has a good number of Ensemble Dark Horses like Judith, Raven, Rita, and Flynn.
Nanaly Fletch is never seen in popularity polls, her story involvement in-game is rather minimal, but maintains quite a substantial fanbase, nobody complains about her... and when there's a Tales crossover spinoff (Radiant Mythology, Versus) she's usually the first character from Destiny 2 to be announced, beforeThe Hero Kyle is ever announced. She's also the only Destiny 2 representative in the Bonus Boss battle in Tales of the Abyss.
And amongst Tales villains, Barbatos Goetia takes the top spot for villainous Dark Horse. He's also one Memetic Badass, provides a challenging fight and is voiced by Norio Wakamoto... guess that explains. His popularity is acknowledged by his numerous cameo appearances in future games, and having the privilege of being the only villain to get multiple roles in the various Tales Of comedy CDs.
Tales of Graces has quirky whimsical scientist Pascal. She provides a lot of the humour in the game, and just lightens the mood, especially when interacting with someone grumpy like Hubert.
Also, Malik for the same reasons as well as his shipper on deck antics.
From ''Tales of Phantasia" there is also the Cute Witch Arche Klein...a certain infamous fan translation probably had something to do with that (at least for the English speaking fandom).
Fire Emblem: Genealogy of the Holy War has Ayra the sword mistress, probably due to the fact that she's one of the most powerful units early in the game due to her Meteor Sword skill. Her looks and attitude (cold, tough, ass-kicking on the outside, but quite a sweety on the inside) also help out. In fact, you can be assured if there's some fans wishing that Genealogy of the Holy War gets represented in other games, if it's not Sigurd, or Seliph, it's her. Finn, also from genealogy qualifies as well. Since he is the only character playable in all parts of the Jugdral saga.
Nino from Fire Emblem also qualifies, taking first place in a Nintendo of Japan popularity poll (ahead of the main characters); many people assume this is for unwholesomereasons, the same poll also show Matthew might be an example, placing ahead of Lyn.
Although he is an optional character who can only be recruited in a sidequest, Canas from Blazing Sword received 7th place in the above popularity poll and is often considered as a must have character. This is likely due to his well balanced stats, being the only dark magic (arguably the best magic in the game) user until the last chapter, his usefulness as a healer due to his magic stat, and being capable of dealing more damage than even Athos with Luna. People also seem to like his curious, passionate personality which contrasts with the typical brooding or evil stereotype of dark magicians.
On the subject of Fire Emblem, Denning, a character who only appears as an optional boss (killing him is not required to complete the mission) near the very end of the game fits this trope. He is found in almost every ROM Hack of Fire Emblem and was popular amongst the Fire Emblem fans, and his one-line vocabulary was found in a lot of people's signatures.
In the same vein as Ayra, Mia (Wayu) from Path of Radiance and Radiant Dawn has an equal fandom without actual importance. The Myrmidon/Swordmaster/Trueblade classes always have some amount of fandom especially when said character is a Genki Girl with a Cool Sword.
The Sacred Stones has Joshua, the game's first Myrmidon. There was a lot of Nice Hat involved, with a side of Handsome Lech.
Path of Radiance has Oliver, a fat and ugly slave trader with an incredibly ironic love for beauty (which he sees himself as the paragon of), who as a boss dies so easily that the only challenge is getting to him before the allied NPCs kill him. He is loved for two reasons: his characterization being ridiculously over the top to the point of hilarity, and his Leitmotif, the famous Power-Hungry Fool. He returns in Radiant Dawn, where he was revealed to be Not Quite Dead, and becomes recruitable.
In Path of Radiance, Sothe was a small (teenager-ish), weak thief with limited use. In Radiant Dawn, Sothe is a strong, developed Loveable Rogue. He appears as one of the main characters.
If we're going by Radiance and Dawn, you can't forget about the silent assassin Volke then. He's pretty damn good at what he does, too.
Radiant Dawn has the 3-13 archer. He's a non-playable AI-controlled character that manages to actually help you out a lot in a difficult chapter of the game.
Fire Emblem in general is chock-full of Ensemble Darkhorses, mainly due to having Loads and Loads of Characters. A lot of them, such as Gheb, Glass and Batta the Beast (minor boss characters in both regards, or so the game's creators would have you think), have been elevated to the status of Memetic Badass.
Fire Emblem Awakening has Owain, who is an incredibly popular character based on how eccentric he is. His catch phrase "down, sword hand!" also helped make him one of the most popular characters.
Admiral ZEX from Star Control II has a surprising amount of appeal outside the main fan site, but he's no Draco in Leather Pants; female fans simply tend to find him attractive for his canon personality. Of course, the Ho Yay with the main character do have everything to do with it... additionally, the first Spathi that the player meets - Captain Fwiffo - is a fan favourite, even though the player basically only has one conversation with him, after which Fwiffo's commanded ship becomes one of your fleet. It is not uncommon for players to keep his ship in active duty and alive for the rest of the game. Why? Just because Fwiffo rocks.
The angsty backstory might not necessarily be it, considering that everyone whose mind you enter has an angsty backstory that provides the basis for their particular neurosis or outright insanity.
He's not emotionless. He only advocates keeping emotions controlled as a means of turning them into firepower to destroy tacky lamps. And that is awesome.
Psychonauts also has D'Artagnan, the original protagonist, who was cut for being hard to render. Nonetheless, he does get a quick cameo reference in the end, and fans seem to have latched on to him as well.
Dart's popularity may have something to do with the fact that the reason he was cut was that his hat was "too awesome" to render.
The Captain, a wannabe-character who only serves as someone Arthas can talk to in the human campaign of Warcraft III has attained many fans among the community. In the retelling of the Warcraft III events in the book Arthas: Rise of the Lich King, he finally gained a name — or actually two, split into two separate characters, Falric and Luc Valonforth.
Speaking of Warcraft, The Horde in general became immensely popular despite being the main antagonist in the first two games for their hilarious Stop Poking Me quotes actually making playing the bad guy more fun, which eventually lead to the Horde's (or at the very least, the Orcs') ultimate redemption in Warcraft III. Since then they've gotten more and more attention from both fans and Blizzard themselves, and are by far the most iconic group in the entire series, almost overshadowing their rival faction, The Alliance (much to their chargin). Blizzard Entertainment has made numerous art, novels, and other media centered around them, as well as their fanmade equivalent, and Blizzard even has an official rock band, the Tauren Chieftains, with songs like their well known "Power of the Horde" dedicated to them. Not bad for a faction that was originally your typical stock orc villains.
Saurfang, Bolvar, and Darius Crowley were all minor characters introduced in World of Warcraft. They have all become hugely popular since their introduction (Saurfang moreso than Bolvar and Darius combined), with the first two gaining more prominent roles in later expansions.
This may have led to Raikov's re-appearance in Portable Ops, this time as a playable character, who despite having limited relevance to the main story, ended up having more lines than in Metal Gear Solid 3.
The Colonel AI from Metal Gear Solid 2 is so popular that he's basically entirely eclipsed the actual Colonel in terms of personality and memorability. Even in Super Smash Bros. Brawl and Metal Gear Solid 4, there were references to the Colonel AI (in 4, this meant an Easter Egg flashback of something Snake couldn't possibly have known about), and the real Colonel's personality was changed to be a little more Cloudcuckoolander to bring it in line with the Colonel AI. The Colonel AI is probably the only thing about Metal Gear Solid 2 that even its detractors liked.
While still a very polarizing character, Raiden got himself an injection of badass as the new Cyborg Ninja in Metal Gear Solid 4: Guns of the Patriots that helped him win over many a fan, including people who despised him in the past. Then he got his own game, and he became even more well liked...
Although they only appeared in two games, the Dynamic Duo of Suikoden, "Blue Lightning" Flik and Boisterous Bruiser Viktor, remain as fan favorites and fans have been wishing that if the chronological setting is correct, they would reappear again. Too bad Konami never thought of that since their last appearance (though, they did get some mention in the third game).
At least Flik and Viktor are still important for the games they appear in. On the other hand, Flik's lover, the one he named his sword after, Odessa Silverberg, only lasts not more than a quarter of the first game before she died. Even then, she was considered pretty cool and well-liked for her short time, even to the point that there was a short story involving her before the events of the first game and she was an all around Badass. Of course fans know that she's Too Cool to Live and her death still contributed to Flik's ascension to a darkhorse.
Black Knight Pesmerga also. He is easily accused as a Palette Swap of Yuber, always joins late and never contributes to the main plot other than 'looking Badass', and his customization option is limited, and he's only in two games. He's still well loved anyway thanks to his links with Yuber which unfortunately never got resolved.
Hai Yo from the second game, your resident chef... who also has his own optional sub-quest (with nothing to do with the main plot) encapsulated with an addicting cook-off mini-game, then he's revealed to also be an Iron Chef, as gameplay-wise, he's highly customizable and can even surpass the aforementioned Pesmerga, just as long as you take your time to train him. With that his popularity soared so much that two characters from that sidequest of his, Retso and Shun Min, end up being featured as Stars of Destinies in the fifth game.
Sergeant Major Avery Johnson from the Halo series of videogames started out as an expendable, randomly spawned Marine. In Halo 2, he is promoted three pay grades at once, from Staff Sergeant to Sergeant Major, hailed as the only survivor besides the Master Chief of the events of the first Halo (despite the presence throughout the game of Gunnery Sergeant Stacker and PFC Chips Dubbo, two other Marine survivors). In Halo 3, Johnson heroically sacrifices himself so Chief can destroy the Flood. There were many Manly Tears during that scene.
Notable about Stacker and Dubbo is that, like Wedge, they both live through the whole trilogy.
The ODSTs deserve some respect. It's even noted that the employees at Bungie consider these guys to be their favorites. With a name like "Orbital Drop Shock Troopers", what's not to like? They even got their own Gaiden Game.
An even bigger Ensemble Darkhorse is Demyx. While Axel does play a prominent role in Chain of Memories, Demyx plays an extremely minor role in the story compared to Axel. (He basically exists to steal the Olympus Stone, and to put an actual boss battle before the 1000 Heartless Fight.) Despite dying relatively early in the game, he has one of the largest fan followings in the game.
This may be partly because Demyx, during the second fight against him, is a Boss among Bosses. Especially surprising since right up until that fight he seemed like such a wuss.
Demyx got a good deal of help in the characterization department when they let Kenichi Suzumura voice him in the Japanese version. Originally, his role was even smaller but Suzumura was allowed to ad-lib and helped expand the character, and even came up with his distinctive death cry.
Another example is Zexion. Despite only appearing in a few scenes for Riku's story in Chain of Memories, being killed off by Axel (off-screen in the original, too) before the end of the story and all in all being unimportant, he has several fanlistings, dozens of fanfics devoted to him and quite a large amount of fanart. The reason behind this is pretty obvious.
Doesn't hurt that Zexion was given an ambiguous death without ever having his weapon or element revealed in the first Chain of Memories game, while apparently being one of the higher-ranked and more important characters in the mysterious Organization. Even Kingdom Hearts II obscured that same information about him. Oh, and, of course, his hair color made him a possible link to both the series duetoragonist and the series' Big Bad. AndBirth By Sleep has him as a mute orphan child, with a seeming interest in the Unversed, taken in by Ansem the Wise - who's also a king. Basically, in most of the games he's been in, he's deliberately presented as a guy with a Mysterious Past, in a manner that usually means that an NPC will return later with even more importance...which, as of Dream Drop Distance, has finally happened.
It could be considered a Touhou tradition for at least one Ensemble Darkhorse to arise per game:
The Embodiment of Scarlet Devil has Hong Meiling, who for a long while was the most popular minor character that was never playable. After several debates about what to call her (which ended with everyone calling her "China") she garnered enough popularity that, at one point, she took the top spot in the game's equivalent of Saimoe. Her popularity led to her being included as a playable character in the first fighting Gaiden Game of the series, but due to her Butt Monkey status she became a Joke Character with no role in the storyline, and with Hisoutensoku returned to playable status as well as finally getting her own story route (she still didn't escape being a Butt Monkey, though).
Cirno is the Ensemble Darkhorse of Touhou, Memetic Mutation (she's the strongestand a genius!) propelling her into perpetual stardom amongst the fans. This led not only to her being playable in Hisoutensoku but also one of only three with a story route (along with Meiling and Sanae), and with Great Fairy Wars managed to get her very own game.
Cute, destructive Flandre Scarlet is featured just as much, if not more, in fan works than the other members of the Koumakan Cast Herd, despite appearing in a grand total of one game (and one Gaiden Game that no-one liked).
And then there's that "little devil" that appeared as a midboss in Patchouli's stage. No dialogue. No name. No profile. Immensely popular. Not quite as popular is the similarly unnamed fairy that appears as the Stage 2 midboss, though that's due almost entirely to her portrayal as being a friend of Cirno (see above).
It could be argued that the bosses in this game are this to the entire series considering that their most featured in Gaiden Games and supplementary material, and by extension, giving them more characterization. Not to mention that any fanwork that features more then a couple specific characters usually have at least one of them. There's also the fact that out of most bosses, the bosses of this game seems to be the most associated with the main characters, with Sakuya herself being a main character until Mountain of Faith and again in Double Dealing Character.
Perfect Cherry Blossom has the Prismriver Sisters. They would later return in Phantasmagoria of a Flower View and frequently appear in various fanworks.
Lily White, a midboss of PCB, also a special Mook in Phantasmagoria of Flower View, is exceptional enough to have received her own profile in Perfect Memento in a Strict Sense (read: official material)! Ran and Chen are debatable depending whether you view Yukari's shikigami as side characters or not. Alice would be considered an Ascended Extra.
Imperishable Night has Tewi Inaba, and Fujiwara no Mokou. Also Reisen, which depends on whether you view her as a main character or a side character.
Phantasmagoria of Flower View has Yuuka Kazami, who is a debatable example as while most of her fans are only familiar with her brief appearance in one game she was also the final boss of Lotus Land Story and playable in Mystic Square (though even that is debatable, as ZUN hasn't confirmed if they're the same character or just him being nostalgic).
Also from PoFV, "sunflower fairy". While being just a Giant Mook, she does have some popularity and fanart.
Mountain of Faith has Nitori Kawashiro to a limited degree, especially after her appearance as a supporting character in the following game. Momiji Inubashiri as well, another nameless, dialogueless, official-artless midboss who has as much fanart as most of the main playable characters.
Subterranean Animism has both Parsee Mizuhashi and Yuugi Hoshiguma. May have something to do with the incredible amount of people that pair them together. Satori Komeiji is also extremely popular; she's been in the top 10 in the annual Touhou Popularity Contest ever since she's been eligible.
Undefined Fantastic Object has Kogasa Tatara. Partly due to the fanbase quickly latching onto her when the demo was first released, partly due to being the only character not connected to the game's plot at all, mostly due to being immenselycute and pitiable.
Tokimeki Memorial had Miharu Tatebayashi, a sweet Shrinking Violet who often crashes into the main guy as a hidden character, but she became extremely popular with gamers. Similarly, assistant Saki Nijino also became very well-loved within fandom, often scoring 1st place in character polls and as such became the heroine of the 1st Drama Series game ; and add to the list AyakoKatagiri, who was popular enough to be the heroine of the 2nd Drama Series game.
Elizabeth as well. In the original release, she was mostly a side-quest hub character, but she gathered enough popularity to receive a fully voice acted personal side-quest in the Updated Re-releasewhich ends with her and the main character sleeping together!. She also obtained additional quests and dialogue, and was another of the few characters from Persona 3 to receive a Shout-Out in Persona 4 through her sister, Margaret.
Both of them pale in comparison to Badass Longcoat Shinjiro Aragaki, who stands as a fan-favorite party member despite only being available for a small fraction of the game. Unsurprisingly, when the PSP update of the game added the option of playing as a female protagonist, Shinji was not only made a possible love interest, but maxing out his Social Link provides an additional bonus: it saves him from his Plotline Death.
Speaking of the female protagonist, Minako is more popular than her male counterpart, despite never appearing in anything related to Persona 3 except the Live-action theater. Is mostly because of her having Social Links with every SEES member (yes, even Koromaru) thus giving the characters more 'development' and because of having the choice of remaining as friends.
Persona 4 has Naoto Shirogane, who doesn't show up until midway through the game and only becomes a party member much later, who is popular for her status as a badass ace detective, her quiet intellect, her slight social ineptitude, and her androgyny.
Kanji, for being a huge, intimidating badass, as well as one of the rare video game examples of an excellently written gay character (maybe.)
Nanako, the protagonist's utterly adorable cousin, to the point that her kidnapping and (temporary) death are considered the game's biggest Player Punch.
Adachi is surprisingly popular considering that he orchestrated the kidnapping and attempted (though sometimes successful) murder of several people (mostly teenagers) and Nanako, on top of being a disturbingly huge misogynist and attempted rapist.
Anthony Carmine in Gears of War, a Red Shirt killed early in the campaign. He was playable in multiplayer, and was so popular that it was very common to fight COG teams filled entirely with Anthony Carmines. In the sequel, Carmine was brought back - or more specifically, his brother, Ben Carmine who has a similar personality He dies as well although he was given more screen time and a dramatic, emotive, death unlike Anthony. Then in the third game, Carmine is resurrected yet again with Clay Carmine, with a running gag about his family's expendability with Clay narrowly avoiding death multiple times. However, Clay does survive in the end.
From the Locust side we have General RAAM. Despite appearing only about three times in the first game and having a much smaller role than Skorge and Myrrah. He is so popular that an entire DLC for the third game is a single-player prequel story where RAAM returns, and is playable.
Among the weapon selection, the Gnasher Shotgun seemingly acquired Ensemble Darkhorse status. It's fairly obvious that the Lancer and its Chainsaw Bayonet, the signature weapons of the series, were intended to be the weapon people relied on most. However, the shotgun was so strong that 90% of the community used it exclusively, and foamed at the mouth when Epic tweaked it in the sequel.
It helps that Henry is a self-aware parody of the kind of cooler-than-thou Foil to the protagonist that tends to become the Ensemble Darkhorse of their respective series.
If the staggering amount of fanart and cosplays are anything to go by, Dr. Naomi is quite loved by the fanbase. Half the reason due to herknockers and all the cool stuff that she provides Travis, including a giant mecha.
On the other hand, Selvaria would go down as the only 1st Valkyria Chronicles character to appear in crossover Project X Zone, albeit as an enemy. She makes it up later by being included in the roster of Dengeki Bunko Fighting Climax for console version exclusives, along with Alicia... but our heroine is delegated as Support role, whereas Selvaria is being the playable one and doing the majority of ass kicking.
To a lesser extent, Marina Wulfstan and Isara are rather popular characters.
He's also the only protagonist who's appeared in games of different time periods, so he has a greater chance of being brought back (as he was for the Sorrow series).
Castlevania: Judgment has one in Golem, who was largely a non-entity in the game, players considered him inconsequential, but they grew a fondness for him in this game, and has what's considered the best story mode in the game. His Iron Woobie status may also have gotten some fandom, too.
As far as Belmonts go, the most popular one is the one that DIDN'T get his own game. Julius Belmont is a canonical Badass, a trait especially elevated in Dawn Of Sorrow where, when asked how he took down the more powerful regenerating monsters despite being unable to draw magic seals to stop the regeneration, he responds by stating he just kills them too fast for them to regenerate. His popularity probably has to do with being canonically the strongest Belmont and indeed possibly the strongest character in the series, having permanently killed Dracula, teaming up with Alucard, having the more well received playable post game quests, being totally manly with a Badass Longcoat and, in Aria of Sorrow, being a combination of That One Boss and Best Boss Ever, along with his theme music. Added to this is the fact that at the time of the Sorrow games, he was in his mid-fifties. Even with the reboot, many fans are still clamoring for a game based on the war of 1999, where he permanently killed Dracula but it was never elaborated how.
Looking back at the Shining series, if there is one character who receives considerable popularity, it's none other than Shining Tears' token ice witch Blanc Neige. She is often hailed as one of the best NPCs to have around (despite being squishy) and possesses a skill that is extremely useful, and many fawn over seeing how she starts out super aloof and bitchy, then warms up and lets out a very cute smile if paired at the ending. Maybe she's not the true main character, but she stands out as the character who received the most fanarts, and also escaped the 'cut', appearing in the crossover with Shining Wind. And if there's one more factor to her popularity, it's her voice in the game, in the Japanese version. She's voiced by none other than Megumi Hayashibara herself.
From the sequel to Tears, Shining Wind, we have Tetsu Inada's own beast king Rouen. He's a Badass who is also a pirate and a king of a Chinese based kingdom.
An older example back from the Genesis days would be the Kiwi, an optional character from Shining Force 2. His stats aside from physical defense is poor, and Magic will inevitably one hit kill him every time. He is a bit of a Magikarp Power type, if you level him to his promotion level, he gains the ability of flight and breathing fire!...But even with this he's still likely to be instant killed by magic due to his horrible HP. Despite this, many players will use him through the whole game, giving him nearly all of the stat boosting items to keep him on par with the rest of the force.
Don't ask us how, but the pre-packaged Frances Worthington III, a student from The Sims 2: University somehow developed a small cult that's absolutely obsessed with him. Per the strangeness that is TS2 fandom, you can't quite tell how serious they really are about it.
Most simmers have a strange fascination with Goopy Gilscarbo, a funny-looking plainclothes townie with allegedly great genes.
A number of Pop'n Music 's many, many, MANY characters have more fans than mascots Nyami and Mimi; Milk, MZD, and Minit's, just to name a few.
Silent Hill has the one and only Pyramid Head. Most likely due to being an utterly terrifying Implacable Man (and Memetic Molester, though surely that's irrelevant) and frequent threat in the most popular and acclaimed of the games, he/it/whatever is iconic to the series. Origins and Homecoming both feature Expys of him, and despite being unrelated to the plot his appearance in The Movie was almost as well-publicized as the film itself.
And Strider Hiryu, who's one of the most requested characters for Marvel vs. Capcom 3, thanks to his previous appearances. To give you an idea, he ended in third place in one of Capcom's poll for favorite Marvel vs. Capcom/Street Fighter characters, with Mega Man and Poison before him. That doesn't sound all that good, until you realize that the poll featured exactly 111 characters. This actually seems to have paid off in Hiryu's favor. While he didn't make the cut (due to licensing issues) for MvC3, fan demand almost singlehandedly ensured that he'd be joining the roster of Ultimate Marvel vs. Capcom 3.
In the SSX games, Psymon Stark. Not only is he one of the more popular characters due to his out-there personality, he's the only one of the new characters introduced in SSX Tricky to return in any of the later games.
Uzuki from Akai Ito. In an official poll asking which couple was the most popular, Uzuki and the main character Kei ended up as number one.
Minsc (and Boo!) from the Baldur's Gate series. Practically the series' mascot character(s).
The main reason for this is because his legendary Cloudcuckoolander tendencies (mostly by relying on Boo to do any thinking beyond "hitting bad guy with BFS") backed up by being a living wall of ham.
They even got a shout out in Mass Effect 2 with Tali (ironically another BioWareEnsemble Darkhorse herself) having a combat line referencing one of Minsc's and a purchasable space hamster for your quarters.
To some, the paladin Keldorn attains this status for the simple virtue of being one of the few D&D paladins ever who manages to avert all their mostcommonflaws.
Imoen started out as a childhood friend and half-sister of the main character thrown in at the last minute (she doesn't even get any banter lines with the party) as a recruitable party member due to playtesting finding the beginning of the game too hard without recruiting the two evil-aligned Ax-Crazy characters you run into soon after. She was even slated to die once the sequel came around, but her surprising popularity kept her alive, and she went on to become the series' Genki Girl and Woobie extraordinaire (not to mention one of the best mages in the second game.)
May Greenfield, from Armored Core For Answer. Practically no characterization, is an entirely optional wigman, and is never seen outside of her mech, but AC fandom in general and 4chan's /m/ in particular have fallen in love with the cheerful teenage girl in the bright green Engine of Destruction.
Whose logo is a smiley face. Unsurprisingly, (fan) depiction of her is with green hair. And busty.
Both Hakha and Radec are voiced by Sean Pertwee, who played a certain gruff and snarky sargeant made of pure Narm Charm who had to be punched in the face, twice, at his insistence, so that his subordinate could superglue his abdomen closed.
Elora from the same era is an interesting example. She was a major character, and mild Love Interest, for the second game but was completely absent from the third except for a cameo. She was meant to pop up in games afterwards but was always cut from the final product. Despite this Elora is a very popular character in the franchise.
Greta, Bentley, and Sgt. Byrd in the second and third games. Trigger Happy, Terrafin, and Gill Grunt from Skylanders
Agent 9 was enough of a Darkhorse that he was going to be a Breakout Character. Alas, his games never saw the light of day.
On a more general note, the First Recon Snipers are pretty popular.
Yes-Man counts as well - it helps that he's voiced by Dave Foley.
Veronica has also become quite popular.
Joshua Graham only shows up in the game's shortest DLC, and his bigger, active role is only by the end. And yet the amount of attention he gets is huge. Helped by the fact he's among the game's biggest badasses, what with getting thrown into the Grand Canyon while on fire and walking it off.
Vault Boy, the amazing retro mascot who appears in Pip-Boy images and Vault advertising.
Harold, who has been in Fallout 1, 2, and 3, and gone from a human to a ghoul, and then finally to an undead un-living tree thing.
Bang Shishigami is one of the more unexpectedly popular characters in BlazBlue. At first it appeared as though he was going to be a ripoff of Chipp Zanuff. By the time the Arcade game came out, he was highly-praised for his hammilyover-the-top hilariousness. He's practically a living Shout-Out to every manly Shonen character designed in the past two decades of Anime history. This is quite surprising that he's usually seen as a clown in-universe (who likes bitching on him) as well as not even considered "important" by ASW themselves (he's considered weaker than Carl, of all people, as a vigilante), although that may change in the future due to story progression. He also enjoys a lot of fanworks.
Also, Taokaka. It wouldn't be a stretch to say that there isn't a single person who hates her, due to her established reputation for being a walking Crowning Moment of Funny. She even lampshades her status in Relius' Gag Reel.
"Tao would never say that because Tao's adorable and friendly and a fan favorite."
Makoto Nanaya used to be this back in Calamity Trigger. She was an NPC who only appeared in flashback sequences, an old friend of Noel's from the academy days. Despite her very limited screen-time and nominal importance to the overarching plot, she got a surprisingly warm reception from the fandom, mostly due to similarities with the above Taokaka note they're both cute animal girls with ditzy, food-loving personalities who play the role of the plucky comic relief. However, her introduction into the main story by Continuum Shift Extend has been criticised as clumsily handled and has made her into a Base Breaker. She has even drawn Canon Sue accusations, although given who the inspiration for her character is, that may be somewhat the point.
Amongst NPC's, Kokonoe and Jubei are darkhorses too. Kokonoe is well loved for her utter snarkiness and the hilarity she brought in "Help me! Professor Kokonoe!", although her darker, Slippery Slope Jumping actual story has also earned her haters. Jubei is universally liked simply because he's probably the only Six Heroes with the least mental problems or emotional baggage and the closest they can get for a Big Good.
The prayers for Kokonoe's fans are answered as she becomes a DLC for Chronophantasma.
Relius is shaping up to be this, gaining a huge amount of popularity just after becoming a playable character. Oh, and this is despite being an Affably Evil villain who performs Mind RapeFor Science! This is probably because despite his status as an important Big Bad Duumvirate, he wasn't as oversaturated in attention as compared to Hazama (who has slowly lost his favor over time and is facing Villain Sue accusations), nor was he the main concern of the main hero (Ragna), thus fulfilling the Dark Horse qualifications. Having one of the two big gag reels from Extend helps, too.
As of a recent popularity poll, Azrael has officially overcome his fellow newcomers (including Kokonoe!) to be included in the top ten most popular characters in both Blazblue AND Guilty Gear combined. DAYUM!
Sindri Myr, The Starscream of the first campaign. A suave Magnificent Bastard who plays everyone else like puppets and voiced by Scott McNeil at his finest, he still remains the most popular and beloved villain of the series despite not appearing since.
Ork Warboss Gorgutz Headhunta, who debuted in Winter Assault as the leader of the Orks and as a textbook example of Laughably Evil got all of the funniest lines. He subsequently returned for Dark Crusade, where his popularity only grew after he still got all of the best lines, and Soulstorm, which... most people pretend never happened. Fans kept hoping he would return for Dawn of War II, even after it became increasingly unlikely.
Winter Assault also has General Sturnn, who, being the only Imperial Guard officer who actually looks like he's been through a few decades of hell, is widely considered the hardest bastard in the galaxy, and his speech at the end of the Guard campaign is well-regarded for its manliness rating.
Eliphas the Inheritor of the Word Bearers Legion, a suave and witty evil overlord (and the only Chaos Lord with the slightest modicum of sense) who graced Dark Crusade but seemed doom to death in canon. Then the trailer for Dawn of War II: Chaos Rising was released, fans assumed the Chaos Lord shown was Eliphas and rejoiced, and Relic scrambled to put him in the campaign anyway as a treat for the fans. Even despite dying again he returned as a playable character for Retribution.
Araghast, despite getting screwed over in the Chaos Rising campaign due to Eliphas replacing the role he would have filled (indeed, in the final product he has few lines and serves no purpose in the story), still has a significant group of dedicated fans who love his endless ham.
Retribution has the entire Ork campaign. All four of the characters have many fans (especially Bludflagg, due in part to much resemblance to Gorgutz) and nearly every mission has at least one hilarious line that solidifies the claim that Orks really are da best.
Yume Nikki has Uboa, The Grim Reaper-like mask thing. And that's not all. Given that the only real "character" is the protagonist herself, the fandom has latched on to a lot of random NPCs and made them its favorites. The usual suspects are: Uboa, Poniko (Uboa's "normal" form as a blonde girl), Masada (a tall figure dressed all in black, sitting in front of a keyboard in a spaceship, with googly eyes), Monoko (a sweet Joshikousei who turns into Body Horror incarnate in the presence of the "Stoplight" effect), and Kyunkyun-kun (a happy rainbow-colored blob who loves to rub poles, and that is not a euphemism).
Basso The Boxman from the Thief games has exactly two canonical appearances: In Thief: The Dark Project he's in Cragscleft Prison, and Garrett- who had to break into the prison for unrelated reasons- rescues him in exchange for a valuable nonmonetary reward from Basso's sister. In a mission from Thief II: The Metal Age, Garrett, somewhat against his better judgement, assists Basso in rescuing a indentured servant that Basso's fallen in love with from her cruel mistress. For some reason, Fan Mission community liked Basso and he gets used as a plot device of creators. Eventually, Fanon evolved that established him as a hapless, bumbling individual who was nevertheless Garrett's only true friend in a Crapsack World of treacherous allies and manipulative organizations.
From the same game series, there's Benny, the incompetent and usually-drunk guardsman. Though he's more of a Running Gag...
Refund Guy comes back in 3. He finally gets his refund of fifteen credits. The clerk says he's never seen someone so dedicated over a toaster.
A few other darkhorses return for ME3, or at least receive some recognition: Aethyta is around the Citadel, and is revealed to be Liara's Father. Charr and Kal'Reegar both come back for massive Tear Jerker. Charr dies fighting the indoctrinated rachni, and leaves behind a poem to be sent to his asari wife/ex-girlfriend; Kal'Reegar sacrifices himself fighting the Reapers. Lastly, Aria comes back to offer you some sidequests. (She also acts as a temporary party member during the Omega DLC, of which she is the central character.)
Also, the Stage 2 flamingoes. Part of a high-scoring secret, the flamingoes have become very popular amongst Garegga fans, despite being little sprites that have no relevance to the protagonists or antagonists.
One of the most popular and interesting characters in Atelier Iris: Eternal Mana is not a playable character, but rather a shopkeeper of all things. Veola, the owner of the magic shop in the first town you visit becomes the most captivating and fleshed out character in the game as the plot progresses. The character in question is also the subject of some fan fiction.
Achmed Khan from Backyard Sports. Originally, he was just a regular playable character who was not on any of the artwork of the first few games. But he got a massive fanbase, mostly due to his guitar-player wannabe personality. This probably led to his inclusion as a playable character in Backyard Skateboarding, and (unfortunately) his Flanderization.
Sengoku Basara is a series rife with Yaoi Fangirls for fans. However, there is one figure that stands to be very popular amongst the boys, and that is... Oichi. Her charm is just how tragic she ends up in her life, with her whole story being a huge Tear Jerker. She also has the voice of Mamiko Noto, and with some other things, she became the series' dear girl and even when Sengoku Basara 3 is announced to have some characters, especially those close to Nobunaga, to be cut... when asked about Oichi's eventual fate, the producers always say "I'm not telling" to tease the fans. Oh, and she's also the sole playable female in the fighting game spinoff. And now she is confirmed to be playable in SB3, despite being historically LONG DEAD before Sekigahara even begins (but then again, this game really doesn't care about historical accuracy, so she's there by popular demand). And then, it gets even better in English when she gets a popular voice actress to voice her: Laura Bailey.
No mention of Oichi's light saber wielding, shield boomerang throwing, justice maniac husband Nagamasa Azai? Along side Oichi, Nagamasa wasn't initially playable in his first appearance in Sengoku Basara 2. His popularity sky rockets him into Playable Character status in the expansion SB 2: Heroes. Even after his canonical death, fans were clamoring for his return. After taking a leave of absence in Sengoku Basara 3, with the story being rebooted, Nagamasa, announced along side Oichi, and his newly NPC sister Kyougoku Maria, are returning in Sengoku Basara 4. It also helps that even history-wise, aside of being Oichi's husband, he's just another warlord that Nobunaga trounced without anything super awesome like other warlords. So for him to explode in popularity in this series... well, that certainly fits greatly.
The Galactic Rangers from Up Your Arsenal. Not only among the only characters that give Ratchet proper appreciation for his work, they promise to pay him back for all his help. During the final boss fight, they make good on that promise. Gets better. They have been confirmed to appear in the film!
Being the protagonist's sidekicks, however, it's understandable that they would have a pretty good fanbase. Dimitri, on the other hand...
What about him? His suit is greasy sweet! His ridiculous mannerisms and oddball use for the Clockwerk tailfeathers (plates in a counterfeit money machine?) made him so popular that he managed to worm his way into the Cooper Gang in the third game.
While the Korean version of the game failed, the characters created for it proved surprisingly popular, especially Mr. Fanservice Foreshadow and Sword and Gun user Spark Blade. Good aversions of Captain Ethnic.
The Jak and Daxter series has a few, but the most surprisingly popular character has to be Jinx. He only appeared in three missions in the ENTIRE series.
The Metroid franchise has Ridley, the iconic Space Dragon. Although he's generally regarded as the Big Bad of the series today, he didn't start off that way; he was originally just a mere dungeon boss in the original game, serving the actual main villain of the game Mother Brain. But in his next appearance, Super Metroid, he more or less steals the show when he comes in and captures the baby Metroid from Samus, prompting her to go back to planet Zebes and rescue it, resulting in one hell of a vicious battle between the two near the end. His role in the story effectively led to him displacing Mother Brain as the true leader of the Space Pirates, and even made out to be responsible for the deaths of Samus's birth parents and her adoptive family, the Chozo. The fact that he also has an incredible awesome theme song also helps.
Kraid may also qualify, despite the fact that the games have given little to no background on who he is. Heck, in the official manga he just appears out of nowhere on Zebes unlike Ridley and Mother Brain, who were given full introductions beforehand.
Upon revelation of Metroid: Other M, fans quickly fell in with love Anthony Higgs, who earned the nickname MBD (Mysterious Black Dude). When the game became a notorious Base Breaker, even those who didn't like the game overall tended to regard Anthony as the best part of it. He's portrayed as Samus' best friend... and unlike the highly contested portrayal of Adam, Anthony actually acts like her best friend, being a kind, supportive person, with a good sense of humor and respect for Samus as a person. It doesn't hurt that he's also a Bad Ass who wields a BFG.
Rundas, the ice-based alien bounty hunter of Metroid Prime 3: Corruption certainly has a large following. Most likely because 1) cool powers; 2) his voice and personality; 3) twice he rescues Samus, once from several Pirate shuttles and the other from falling to her death after battling Meta Ridley; 4) out of the three hunters, he seemed to be able to control his corruption the best, well enough in fact that Dark Samus had to take control of him herself to fight Samus; 5) his hauntingly sad and beautiful boss theme.
Of all the bounty hunters that appeared in Metroid Prime: Hunters, Sylux, only referred to as an 'it' seem to be the most popular. And the ship that appears to follow Samus in the Metroid Prime 3 ending looks very similar to Sylux'.
In Ōkami, the Ensemble Darkhorse is probably Oki, who is very much of a Bad Ass, take into account he has one of the best fights in the game, is probably one of the characters with the most personality, and he can turn into a wolf, yeah, he's that awesome. Waka probably counts too.
Tobi is also very popular, despite showing up for only one dungeon and in essence being A piece of paper. So popular that the HD port of Okami gave him a trophy, despite normally being set aside for slightly more major events. Most bosses get insults. Tobi gets "Rest In Peace".
Eversion might have not won the Commonplace Book competition at the Tig Source Forums, but became more popular than Verge (the winner) and From Primordial Egg (2nd place; Eversion was the third). Apparently, it all began when the game got posted at the VG Cats homepage...
F-Zero GX/AX gave us the AX racers. Each are unique in every way possible from the already massive set of 30 unique racers.
More or less, the series could be summed up as "CaptainFalcon + Everyone Else". There's a favorite out there for everyone.
Assassin's Creed I gave the gaming public Malik, Jerusalem quest giver. He has established himself as a fan favourite, mainly for being bitter, sarcastic, and delightfully mean to Altair.
Even more extreme is his brother Kadar, who exists only to get fridged fifteen minutes into the game. He still gets into a lot of fanart.
Cesare Borgia garnered this, mostly for being a male example of Evil Is Sexy it seems. Deviantart has lots of fanarts showing him molesting Ezio or the poor, scared shitless Leonardo Da Vinci.
Damascus' Rafiq (who apparently has no name). He's a...talkative, odd sort of guy.
Rafiq D: Whose life do you come to collect today?
Alta´r: His name is Abu'l Nuqoud.
Rafiq D: Oh, the Merchant King of Damascus! Richest man in the city! Quite exciting, quite dangerous! I envy you, Alta´r—well, not the bit where you were beaten and stripped of your rank—but I envy everything else! Oh, except for the terrible things the other assassins say about you; but yes, aside from the failure and the hatred, yes, aside from those things, I envy you very much!
Meii is one of the more popular characters in the fandom, following only behind the main characters. She's liked far more than her fellow NPCs in the game's Mission Control. However, she's also a voluptuous, blue-furredCat Girl, which explains a lot.
There's also Yoa, one of the Heartwarming Orphans from the lighthouse. Among the six orphans, she's easily the most popular—probably because she, too, is blue, with unusual facial markings, speaks a mysterious language, and seems to be either an excellent snoop or have psychic powers. Her cool design and air of mystery make her very popular with the fans, despite her being just another NPC otherwise.
Several in the Deus Ex series, especially with (optional-encounter) characters who have much more backstory and impact than meets the eye:
The Morpheus AI in the original game is an optional encounter that is "rewarded" by picking a few locks (that you may have spent as much as or more time doing, depending on how you did it and your skills) and an insignificant number of skill points. The conversation he has with the protagonist is considered one of the game's most interesting conversations, raising some interesting philosophical ideas. One of the games most quoted lines is the AI's idea that "God was a dream of good government".
The NSF soldier you find locked up in the UNATCO secure holding facility when JC is imprisoned a third of the way through the game. Despite the fact that nothing in the game indicates you should go out of your way to save him, he's a One-Hit-Point Wonder, and you don't get any reward for helping him get to the Liberty Island helipad besides his thanks and a mention that he can "make it from here", many players choose to save him rather than leave him behind (and spent the whole time escorting him) because the character is ridiculously charismatic and innocent.
Aimee, the homeless woman you meet when you first go to Paris, who asks you to kill the greasels who murdered several of her cats. The character has received a Memetic Mutation for her victory cry (when you complete the missions) of "You saved mah kittehs!" in a heavily-accented French voice.
Malik in Human Revolution, who mostly exists as your comm support, but proved to be so popular that players would go back and replay the Hong Kong crash mission to save her life (and prevent her from being killed and harvested for augs).
Puyo Puyo has Draco Centauros. She was just a random mook and actually the first (normal) enemy, but was so liked she got upgraded to one of the hardest enemies in the sequel and then to outright a playable character with her own story mode along Schezo. Then the franchise reboot came and all old characters were gone (immediately qualifying for this trope). Then they made 15th anniversary, which brought up the old main cast and a few others... but not her. Fan reaction managed to bring her back up for the next game... And even have other two other fan-favorite characters make a cameo!
The third season of the Sam & Max: Freelance Police games introduces Sal, a six foot tall cockroach. Sounds disgustingly unappealing, right? Yet his kind, simple personality makes him such a likeable Gentle Giant that no one can help but love him, even Sam and Max themselves. People can't help but feel guilty when they have to beatthecrap out of him later. Or when he dies in a Heroic Sacrifice, Redemption Equals Death moment, but it's you who persuade him into it.
In Agarest Senki for the protagonists of the five generations, Thoma himself is the most well-liked of the 5 protagonists followed by Leo. For the other party members, we've got Fyuria, Valeria (enough to be brought back to Agarest 2), Silvi, and Murmina.
Kanpachi from Cave Story is merely a fishing Mimiga who isn't much important, until he manages to catch a key for you. Mirai Gamer fandom seems to raise him to Memetic Badass levels.
How can we mention Cave Story without bringing up Balrog? OH YEAAAAAH!!!
Raven/Toona from Rune Factory 3. She's so popular that she beats out all the other female love interests in the series. Following her in a close second is Pia/Persia.
Raven's one of the four heroines in the first OP (alongside Marian, Karina, and Kuruna), she's the second heroine introduced, and she seems to be brought up in conversations a little more often than most of the other heroines. ("Isn't Raven adorable?") I don't think that her popularity came as a surprise to the creators. Pia and Sofia fit the "ensemble darkhorse" bill a little better.
Saturos also has a great deal of popularity, despite dying in the first game and, you know, being a bad guy whose motivations weren't even clear until long after he was dead. Saturos was so popular that it caused fan hate for Agatio in The Lost Age, just because he wasn't Saturos.
In Dark Dawn, Sveta is actually the main focal point of the central plot. Kind of odd considering you don't recruit her until roughly half way through the game.
Sveta gets this from the fandom despite being the Spotlight-Stealing Squad of Dark Dawn. Because in stealing the show, she ended up with more Character Development than anybody else in the series thus far, and is a genuinely likeable character.
In Sid Meiers Pirates The Indian War Canoe. This is the tiniest, puniest ship in the game, used only by Indians to make raids against ports. However, in the hands of the player, it is a war machine - forgoing cannon-play entirely to go for a quick boarding, dodging between cannonballs. Players skilled with Fencing can pretty much defeat any ship this way, no matter how large, and very quickly the ship became a cult favourite, especially for playing at the highest difficulty levels.
Origins has a list of quirky party members, but it's Duncan who's the character that all the fans of the series love. A big reason because he was Too Cool to Live.
Finn and Ariane, the two companions from the Witch Hunt DLC, were incredibly well liked by players.
Cullen, despite only having a few lines of dialogue in the original game, remains one of the most popular characters from it—mostly for the crush he has on the female mage Player Character. His popularity was so great that he returns in a major NPC role in Dragon Age II and is confirmed to return in Dragon Age: Inquisition.
Bann Teagan has many admirers in the fandom, as he's one of the few unambiguously heroic characters, never steps on the player's toes, and even flirts with the female Warden.
Sandal, the simple enchanter son of the camp merchant, is fun and energetic and memetic enough that the fandom very fondly looks on him. There's also the air of mystery that surrounds him and his apparently being a supreme badass when no one's looking considering he's able to wipe out hordes of darkspawn, Templars and abominations.
The (very) minor character Lilley from the "Inside Job" sidequest (who has about 10 lines of dialogue and gets killed off halfway through the quest) has somehow endeared herself to a lot of fans, some of whom go as far as to suggest she should have been made a permanent party member. This is probably all thanks to a surprisingly powerful performance from Alix Wilton Regan, though her being a good-looking Action Girl likely helped a lot, too. There's a possibility that Lilley was supposed to have played a much bigger role in the cutCoterie questline.
Athenril seems to have attracted a similar following, probably for much the same reasons, and the fact that she's one of the elves people will hold up as a sign that the new elf design is good.
Ketojan. He really gave the feeling that he was going to be a party member, which meant his fate left a lot of players very disappointed.
Rex, Ranger Ken, Maurice, and even JULIUS probably count.
In Neptunia, Noire is consistently high in the polls. Appropriate, seeing as the series has primarily been on the PlayStation brand. Falcom is also pretty popular amongst the cast. For the villains, Brave The Hard is the highest ranked among all of them, and for NPCs, it's Histoire.
The Soul series has Li Long (from Soul Edge/Soul Blade) due to his flashy moves, Hwang for being better than his replacement to the point where fans are petitioning him to be included inSoulcalibur V, and Talim due to her kind personality. Shura (from IV) is also very popular despite being a bonus character to the point where many fans were disappointed when she was confirmed not to be in V. Among the Guest Fighters, Link was the most well received by fans. Many even hope future installments of the series hit a Nintendo platform just so he can be included in it. He also singlehandedly ensured that the GameCube version of Soulcalibur II sold more than either the PS2 or Xbox versions.
Ezio Auditore, the Guest Fighter in V, seems to have dethroned Link, believe it or not. In a series where guests (barring the aforementioned Link) are massiveBase Breakers, not only is Ezio noted to be the first guest who completely fits the atmosphere of the series, but he is generating so much hype that he is creating a Just Here for Godzilla effect from both Soulcalibur and Assassin's Creed fans. To put this into perspective, his reveal trailer shows the return of series Big BadNightmare. Ezio completely steals the spotlight, to the point that Nightmare appears to just be an afterthought.
Baten Kaitos Origins gives us Guillo, Sagi's magical puppet sidekick. Aside from having several Game Breaker specials and items, Guillo is widely considered the best character in the game, being a hilarious Deadpan Snarker foil to Sagi, having a compelling backstory, and just generally being a total badass.
Tawna garnered a rather large fanbase, but appeared prominently in only two games and made very minor cameos in others (due to the Creator Backlash concerning Executive Meddling bowdlerizing her original character design).
Fake Crash, a random version of Crash that was meant to be an in-game joke turns into a total fame by the Japanese that makes him now a tag-along guy.
Augus from Asura's Wrath is easily one of the more liked characters in the game, as his boisterous personality and relatively manly and badass traits make him quite a popular character even after Asura defeats and kills him. Many fans clamour for him to be playable in extra scenarios or DLC.
Draven has become this VERY QUICKLY, because that's so Draven. He then went on to obliterate all comers in the GameFAQs 2013 Character Battle, making a strong statement early on by defeating Link, the highest ranked member of the Character Battle's "Noble Nine" (nine characters who used to only ever lose to eachother in 1-on-1 matches).
The series has Loads and Loads of Characters, many of them being incidentals or one-offs worth only a single Jiggy. Nonetheless, some of them get to be quite popular. Prime among them are Chilly Willy and Chili Billy, the twin bosses of Hailfire Peaks in Tooie. In a world of goofy and cartoonish creatures, they stand out because they're enormous, screen-filling DRAGONS, with massive glowing spikes (visually impressive by Nintendo64 standards), epic music, and dialogue that's pretty funny by the standards of an already comedy-centric game.
Mr. Patch, another boss from Tooie, is almost as popular. Once again, his epic boss fight may have something to do with this, as he's easily the largest character in the entire series, and has to be fought while flying. He also manages to be quite funny (how many other characters' Boss Subtitle calls them a "Strange Wobbly Inflatable Thing?).
Sexy Grunty. During the game over sequence of the first game, Vain Sorceress Gruntilda gets her wish to become beautiful. And boy, does she ever! Naturally, she became popular due to her sheer, overwhelming sexiness... and perhaps for the large amounts of Nightmare Fuel said game-over was capable of inducing, particularly "Ugly Tooty."
Clanker, the giant mechanical shark/whale thing from Clanker's Cavern in the first game. Despite his scary appearance, Clanker is one of the more pitiable characters in the series—he's forced to serve as Grunty's trash compactor in a tiny, confined cavern full of grimy water, when all he wants to do is breathe fresh air and swim free.
Varla Guns from The House Of The Dead Overkill. The PS3 version even has two exclusive chapters where you play as her, because people loved her so much on the Wii version.
Yoyo from Jet Set Radio became this when he was Rescued from the Scrappy Heap in Future. Although he is kidnapped for 1/3rd of the game, he's the most popular character amongst the female gamers, and you'll be surprised by how much fan art and fanfiction he has. Cube, the goth girl, is this for the male gamers.
Chuck also is liked by the fandom despite appearing only half-way through Episode Three and being killed off relatively early in Episode 4. Most of the love stems for being a Cool Old Guy and badass, shovel-wielding grandpa with really good and pragmatic advice towards raising Clementine.
Bain from PAYDAY: The Heist grew into this trope, being well known for having planned each heist carefully and how he can get your crew out of custody/jail no matter how many cops and civilians you killed.
Every edition of the Harvest Moon series (with the possible exception of the Gameboy editions) contains at least one, usually a popular non-marriage candidate. Some of the more prominent examples include Pastor Carter (from the Mineral Town games), Flora and Carter the Archeologist (the Wonderful Life versions), Marian (Grand Bazaar), Alisa (Island of Happiness/Sunshine Island) and Eileen (The Tale of Two Towns).
Marriageable darkhorses (usually male) include Cliff (Mineral Town), Vaughn (Island of Happiness), Chase (Tree of Tranquility), Dirk (Grand Bazaar) and Cam (The Tale of Two Towns).
Clive Handforth from Little Big Planet 2. He's a nigh-impossible-to-hate combination of adorable character design (he's made of office supplies!), varying degrees of cynicism, and tendency to utter the best lines in the game. Perhaps if he'd cheer up if he knew he had so many fans! Or not.
Out of the many Puchirus monsters in the obscure DS game Puchi Puchi Virus. A Sea Bee, a goldfish/bee hybrid Puchirus monster, inspired more fanart than other characters.
Sweet Tooth from Twisted Metal and, to a lesser extent, Grimm and Dollface. Sweet Tooth was just another character in the original game among an already colorful cast. Now he is the face of Twisted Metal. Grimm has been a recurring character in the series, and Dollface has quite a following. All three are the main characters in the 2012 Reboot, and Dollface was an unlockable mascot in Playstation All Stars Battle Royalenote Grimm was added later as DLC.
Deadly Premonition has a few, given its large cast with fairly expansive backstories; of the "visible" cast, most notable is probably Carol. She's one of the few people in the seemingly sweet Greenvale who's as as acerbic as the protagonist, not to mention her stylish choice of dress, the fact that she's a lounge singer, and her very, very strong Yandere tendencies.
Even moreso in certain ways is Punk York. During one small conversation, York offhandedly mentions that he used to dress like a punk rocker in high school. The idea completely captivated fans' imaginations, producing many pieces of fanart of a teenaged, punk-dressed York, and "punk York" was among the more requested alternate costumes for the Updated Re-release.
The dinaurians from Fossil Fighters. A little more than halfway through the first game, it concludes its To Be a Master plot with the main character actually becoming a master, and shifts focus to a group of dinosaur-like aliens who want to take over the Earth. Their plot wraps up, and they don't appear at all in the sequel (save for in some Downloadable Content). However, almost the entire fandom for the two games revolves around them, especially the more saurian Battle Forms they can take, composed of Hard Light.
Homeworld's Kadeshi are a Darkhorse species or rather culture. Whether or not the Kushan eradicated them is a subject of debate.
Victor Sullivan from the Uncharted series has gained quite a bit of popularity, being the favorite character of many, even over the holy Nathan Drake himself. He was mainly taken out of the second game, much to the fan's dismay. No worries, he returns as a main character in the third game.
The Puffstool and their Mushroom Pikmin (AKA Toadmin, Puffmin, etc, etc, etc). Three appearances in the entire series, all in only the first game and two of them being in the game's challenge mode. Despite that, they serve as Fan Fic Fuel and the mushroom-itized Pikmin have a lot of fan art. Some fan art of group shots of Pikmin even include the mushroom variety as sort-of eighth ranger to the established red, yellow, blue, purple, white, rock, and winged varieties.
The Waterwraith is probably one of the most memorable bosses in the second game, due to being so different from everything else. For starters, it is considered one of the biggest sources of Nightmare Fuel in its game, as in any of the first sublevels of its dungeon, it will crash down and start chasing you after an invisible timer reaches its limit. Then there's the actual fight with it, where after getting Purple Pikmin its rollers will eventually get broken and it's revealed that the thing is actually a Dirty Coward. This probably got a nod in the third game, where the final boss seems to be related to it. How, though, is even more Fan Fic Fuel on its own.
The prosecutors in the Ace Attorney franchise (sans Payne) tend to always be incredibly popular. Edgeworth and Godot in particular. This is probably one of the main reasons why Edgeworth is the protagonist of the Investigations games.
The detectives in the games tend to be popular as well. Gumshoe for his funny personality, Ema Skye for her Adorkable personality, and Fullbright for his hammy and For Great Justice personality as well as being the Big Bad of Dual Destinies in disguise.
Out of the four animatronic animals present in Five Nights at Freddy's, the one who seems to get the most love from the fans is Foxy the Fox Pirate, whose unique behavior pattern and design have made him a definite fan favorite for many. Most of the fanart for the game that isn't of more than one of the animals is of him; he gets more attention than Freddy himself! All of this, despite the fact that he was entirely absent from the game's trailer, and the player isn't officially informed of his existence until the second night.
Andriy Kobin. He's an outright villain in Conviction, having kickstarted the game's plot by revealing that he was the one who killed Sam Fisher's daughter (he isn't, and she's still alive) as well as shooting either Archer or Kestrel (the latter revealed in the next game to be Not Quite Dead) at the end of the co-op campaign. After getting a satisfying No-Holds-Barred Beatdown from Fisher, he's incapacitated and presumably forgotten about, but he made enough of an impression on the audience that he was brought back for Blacklist. This time, he gets much more dialogue, has his own set of side missions and undergoes a Heel-Face Turn, helping the Paladin crew when the ship is hit with a computer virus and later becoming a bonafide part of the team by the final cinematic. Being voiced by Elias Toufexis (Adam Jensen from Deus Ex: Human Revolution) helped too.
Likewise, Kestrel (one of the two playable characters in the co-op campaign). He's a badass Voron operative who's calm under pressure and talks very little. He was enough of a fan favorite that his death was retconned in Blacklist to have him be placed in a medical coma instead, and the final co-op mission has Sam and Briggs rescuing him from the gulag he's been placed in. It even gives a Sequel Hook for his character after he's brought back to the Paladin.