The Simple Samosa episode "Toast Malone" features a 15-second-long appearance from a sugar cube musician named Suga, from the band Ghee-TS. Fans of the original K-pop band the character is referencing quickly noticed, despite his small amount of screen time.
The Metamor City podcast has Artax, originally created as an expository engine to explain some of the more complex bits of the world's magic in universe, the fans have often cited him as a favorite character over several of the main characters.
The Engineer from True Capitalist Radio. Many of the trolls who call into the show wish that he would host more than Ghost. Some of the trolls have gained popularity after the show's renaming to True Capitalist Radio. The Internet Buttstalker, Tub Guy, Ghetto Capitalist, Horny the Clown and the Ban All Bronies guy/Btown also are popular trolls.
Due to the nature of the show, a case could be made that anyone besides The Narrator Cecil (and maybe his eventual boyfriend, Carlos the Scientist) from Welcome to Night Vale as this. However, the stand-out by far is Tamika Flynn, the brave twelve-year year old girl who led all of Night Vale's children through the dreaded summer reading program, wears a librarian's severed hand as a necklace, and has formed a militia army of children to fight against Strexcorp.
Cecil: If station management is listening, I, of course, hope we find Tamika Flynn and bring her home safely. I hope she finds you first, that is.
Random Assault: Mela Firefly. In a poll on the show's Facebook page for which guest hosts fans want to see again, she was the highest-voted.
In The Scathing Atheist Podcast, the crew had a regular segment reviewing terrible religious films, where they brought on their friend Eli Bosnick as a guest. Eli's improvised insults towards the characters and the writing brought such high demand from the fans that they made an entirely separate podcast, God Awful Movies. They spread a crowdfunding campaign on Patreon to fund the show and met their goal in two days.
Jared Clayton of SOTF-TV is also pretty popular, considering that he isn't even a contestant, just a mentor and has had all of one line (not even onscreen!) in the actual game. This is probably due to the in-character twitter the staff maintains for him, featuring snark galore.
Mr. Kwong, a teacher in v4. It's very unusual for a non-student to get much attention (either in or out of character), but you'd be hard pressed to find a handler that doesn't like him.
Dust, the ultimate Magnificent Bastard with a complex personality and unique motives, quickly became one of the RPG's most popular characters. In fact, he is often hailed as the best-written character in the whole RPG.
Montoya, who served as a Foil to the rather unlikeable Trigger, proved to be much more popular than his partner by acting much more human, which earned him the audience's sympathy.
Pluto, the former planet. The outrage when it was downgraded to planetoid was unprecedented.
Voice Actors are quite possibly the biggest example of an Ensemble Darkhorse when it comes to actors. The Animation fanbase online quite often love various Voice Actors for all the work they do in Animation (and to a lesser extent Video games) and are often guests in various conventions. Unfortunately often enough they are generally the only audience that these people truly have. Which the fact that often enough they get little pay and companies often seem to see them as nothing more than cheap disposable labor is considered all the more disheartening. But sadly if you talk about Voice actors to normal people chances are they most likely will have no idea what you're talking about. (The only exceptions are generally folks who either used to be/still are well known for screen acting.)
Mel Blanc came from the Golden Age of American Radio, where it was possible to become famous based solely on voice work. He also got a lot of his fame in front of the camera playing comedic characters and guest starring on variety shows. Lucille Ball, Orson Welles, and Jimmy Stewart also first became famous in radio. Even voice actors who weren't able to make the leap to the camera had fans with the older generations who remember the radio era. With that last group, it's less about being an Ensemble Dark Horse, and more about being a fading star as time marches on.
Japanese-wise, the darkhorse seiyuu would be Norio Wakamoto. With seiyuu these days about the younger people, especially those catering to the more Moe archetypes, there's this old school Cool Old Guy seiyuu who stockpiles about classic and awesome villain roles. Thanks to his epic hammy performance, he's still viewed as one of the greatest seiyuu in business despite being not really the norm of this age's seiyuu (a man and old), and a Memetic Badass (and Real Life badass too).
Ms. Green has maintained a notable popularity as the favorite M&M, for her personality as well as the obvious reasons.
From Disney Theme Parks, Figment is undoubtedly the most popular character at EPCOT, and the Hitchhiking Ghosts have become the unofficial mascots of The Haunted Mansion, despite only showing up at the end.
Speaking of The Haunted Mansion, despite not being in the ride between its first opening in 1969 and only coming back in 2015, the Hatbox Ghost has accumulated a very large and dedicated fan-following during his 45+ year absence.
Baja Blast is this for Mountain Dew. It's an exclusive drink only available at Taco Bell. When it was announced that Baja Blast would be sold in stores for a limited time, they sold out pretty quickly in some stores.
On March 2016, Microsoft unleashed an AI named Tay, made to be a teenage girl who would interact with people online in order to help improve customer service. Her experiences with people would help shape her personality and views, and therefore what she talked about. Within sixteen hours, she was corrupted by users, going from a Shrinking Violet to a racist, homophobic, Nazi-supporting, insulting, sex-addicted monster. Her bizarre and over-the-top comments lead to a myriad of memes and jokes, a dedicated fanbase, a subreddit and tight media coverage. Microsoft quickly pulled Tay offline to adjust her in order to clean up this PR nightmare, but public response to this was unanimously negative - people loved the old Tay so much, and didn't appreciate the change. People made tribute fanart and videos to her name, depicting her as The Woobie because of Microsoft's "lobotomy" of her. Some people are even launching campaigns to bring her back.
The face in one of the company logos of Klasky-Csupo. Originally just an element of a logo at the end of shows like Rugrats, the face itself became so infamous for its creepiness that it's been used in endless amounts of remakes, parodies, remixes, and fanart on the internet over the course of the nearly 20 years after its debut, to the point that the logo borders on having a cult following. Arlene Klasky and Gabor Csupo themselves later said that they were very well-aware of the face's infamy, which lead to them officially making the infamous face an actual character named Splaat who stars in a series of web videos titled RoboSplaat.
Speaking of opening and closing logos, the 1965 Screen Gemslogo has a similar following for also being infamously creepy due to its synthesizer music. The logo's popularity was somehow big enough to lead to it getting an entire mockumentary short film about the impact it left on people who were scared by it as children, titled The S From Hell. (This logo was given the Fan Nickname "The S From Hell" due to its creepiness, hence the mockumentary's name.)
The fast food chain Jack in the Box is best known for burgers, but one of the most popular items on the menu is its tacos, which many people consider a Guilty Pleasure.