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Many given the show's long run.

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    Classic Series Debut 
  • The Daleks definitely qualify. In 1963, nothing even remotely resembling them had ever been seen before, and their stellar popularity caused them to be upgraded from one-time Monsters of the Week to return appearances in season two and season three. They were Killed Off for Real in season four, but by that time, Joker Immunity had firmly set in. In fact, the series' developers originally wished to avoid stories about bug-eyed monsters or robots, intending to tell more grounded stories teaching children about science and history. They were reluctant to make "The Daleks" at all, yet it was the serial that made Doctor Who a success. They've grown into their hype, becoming gods of destruction capable of almost making universe-destroying plans work. Massive armies descending on the universe and destroying all in their path is common. And it is awesome.
  • The Celestial Toymaker. His only appearance was in one story in the Classic Series, of which three of its episodes are now lost, but he's still one of the most iconic villains in the franchise.
  • Griffin the Chef from "The Enemy of the World". His constant pessimism and regarding the crazy world around him with resigned acceptance does a quite lot to endear him to the audience.
  • Colonel Lethbridge-Stewart was originally intended as a one-shot character in "The Web of Fear", and Jamie MacCrimmon was originally intended as a one-shot character in "The Highlanders". Colonel Lethbridge-Stewart became Brigadier Lethbridge-Stewart, companion at one time or another to every single Doctor in the Classic Series, longest-running companion in the show's history, even showing up on The Sarah Jane Adventures. Jamie, meanwhile, went on to become the Second Doctor's longest-serving companion, featuring in all of his stories bar one (his first, "The Power of the Daleks"), and making return appearances in "The Five Doctors" and "The Two Doctors".
  • Despite the fact that only under a minute of footage of the villainous duo of Quill and Oak survives from the missing episode "Fury from the Deep", the chilling scene of them attacking Maggie Harris has cemented them as two of the most iconic villains in the show's history. Their creator, Victor Pemberton, seems to have agreed: he actually tried to pitch a spin-off with them as the leads.
  • Bill Filer and Pigbin Josh of "The Claws of Axos" have received their own little fan-gatherings.
  • The Zygons have proved to be a popular creation even though they only made one televised appearance in the classic series in 1975. David Tennant has said they are his favourite monsters, and are so popular that they had their own subplot in "The Day of the Doctor", followed by a Series 9 two-parter that continued it (and yielded up a darkhorse among Twelfth Doctor antagonists with the rebel leader Bonnie, aka "Evil Clara").
  • Sutekh is also quite popular in some circles despite appearing in only one story. It helps that he has a terrifying voice, is a villain powerful enough to take over the Doctor, and this story is widely considered one of the best.
  • Castellan Spandrell from "The Deadly Assassin" is easily one of the most popular Time Lords, thanks to his being a Reasonable Authority Figure in a story filled with corrupt old politicians, as well as his actor's memorable Czech accent.
  • Jago and Litefoot from "The Talons of Weng-Chiang" were basically the Vastra and Jenny of the era. The BBC even considered giving them a spin-off. And they ended up getting one in Big Finish Doctor Who.
  • The Raston Warrior Robot from "The Five Doctors". It only appeared in one scene, but the scene in question saw it take out a squadron of Cybermen.
  • The Mara only appeared in two stories, yet they're two of the most highly regarded stories of the Fifth Doctor era.
  • Despite Sharaz Jek only appearing in "The Caves of Androzani" and dying in the final episode, he's arguably one of the most popular side characters in the show's history. The Cool Mask in particular made him quite unforgettable.
  • Sil from "Vengeance on Varos" was hailed as one of the standout monsters of the Colin Baker era, so much that he was brought back for "Mindwarp".
  • Orcini from "Revelation of the Daleks" for being a genuinely noble badass, to the extent that many see him as the true hero of the story.
  • The Rani, despite appearing in only two stories, (or three if you count "Dimensions in Time"), is one of the most popular villains of the classic series, in no small part due to Kate O'Mara's performance. Fans are still waiting for her to appear in the modern series.
  • The Valeyard from "The Trial of a Timelord" is popular due to his role as the Doctor's Evil Counterpart, more specifically the darkness between the Doctor's twelfth and final incarnations. His popularity only grew when "The Time of The Doctor" revealed that the Tenth Doctor was said twelfth incarnation, meaning that any subsequent incarnation can potentially be the Valeyard.
  • The Special Weapons Dalek from "Remembrance of the Daleks" is one of the most popular Dalek designs, despite appearing in only one story of the classic series. Due to its popularity it has cameoed in the revived series, in the 11th Doctor episode "Asylum of the Daleks" and the 12th Doctor two-parter "The Magician's Apprentice"/"The Witch's Familiar" — the latter being the only story in which the Special Weapons Dalek has a line of dialogue.
  • Despite only making one televised appearance ("Battlefield"), Brigadier Winifred Bambera is very popular among the fandom due to Angela Bruce's portrayal of a capable, tough, no-nonsense, authoratative black female high-ranking military officer at a time when such roles were extremely rare. So much so that she would ultimately be brought back by Big Finish decades later for some audio dramas.

    Revival Series Debut 
  • Despite him only wearing them in one two-part episode, the Tenth Doctor's 3D glasses are a well-loved fan favourite. He is often depicted wearing them in fan art.
  • The Adipose babies from "Partners in Crime". Tumblr fans post pictures of themselves with the cute little walking fat!
  • Within just one episode, the Weeping Angels were heavily regarded as the show's most terrifying villains. Even more so than the Daleks, just from the sheer paranoia factor. "The Time of Angels"/"Flesh and Stone" only increased their popularity (except among certain fans who screamed "ruined" at some of the changes).
    • Sally Sparrow gained a lot of fans after her appearance. More than once, it's been suggested that she be the next companion. Of course it doesn't hurt that Carey Mulligan, the actress playing Sally, is extremely attractive. It helps that Mulligan has gained more popularity outside of Doctor Who as a rising Hollywood actress, with an Oscar nomination for her work in An Education and much acclaim for her work in films like Shame, Drive (2011), and The Great Gatsby.
  • Jethro Cane from "Midnight". "We've broken down! In the middle of nowhere!" Possibly due to the fact his actor is Merlin.
  • "Silence in the Library"/"Forest of the Dead"'s Monster of the Week, the Vashta Nerada, have turned out to be one of the most popular in the entire new run, arguably only being bested by the Weeping Angels. A loyal section of the fanbase has been clamouring for their return.
  • Jenny "The Doctor's Daughter" is one of the most influential characters both in-universe and out-of-universe. Many are still vouching for her return as a companion. Finally it was confirmed that Jenny would return in 2018 in four Big Finish audio stories with the original actress voicing her. That same year also brought Jenny's appearance in comic book story Four Doctors.
  • Wilfred Mott. Initially intended as a one-shot newspaper vendor called Stan, rewritten as Donna's grandfather before becoming the Doctor's companion. Also the Tenth Doctor ultimately dies saving his life.
  • Eleven's fez and bow tie. Both are cool. The fez returns in Series 11, still popular with the Doctor.
  • The Ironside Daleks from "Victory of the Daleks", being among the only Daleks to outsmart the Doctor. Plus they make a pretty mean cuppa:
    "Would you care for some tea?"
  • Craig Owens, the Doctor's roommate in "The Lodger", who gained a lot of popularity based on the excellent chemistry between James Corden and Matt Smith. People were happy when it was announced that the Doctor would go back for a visit and he becomes a companion for an episode.
  • Canton Everett Delaware III from "The Impossible Astronaut"/"Day of the Moon", partly because it's very hard to forget an ex-FBI agent from 1969 who wants to marry a black man.
  • The Paternoster Gang is one terrific trio. They were well-received enough to be used to help bridge the transition from the Eleventh Doctor to the Twelfth, and warranted a short story feature in the kid-oriented Doctor Who Adventures.
    • Madame Vastra, the Lesbian Victorian Silurian Detective, and her wife/servant Jenny are incredibly popular, with the fandom begging for a spin-off. What's so awesome about them? Well, Madame Vastra is a female Silurian. Living in Victorian London. In a mansion. And she works for Scotland Yard, hunting down criminals. And eating them. She's in a lesbian/inter-species relationship (later full-on marriage) with her kick-ass maid-servant Jenny, and they both wield katanas. They're simply amazing, and we didn't even get to see how they met the Doctor, and it's doubtful we ever will.
    • Strax, the disgraced Sontaran Warrior forced to become a nurse, and later Vastra and Jenny's butler in Victorian London. Despite his new station he has lost none of his Proud Warrior Race Guy tendencies and casually informs people he's healing that he hopes to destroy them for the Empire one day. He's also been genetically altered to produce breast-milk for infants and has declared war on the Moon. Pretty much any scene with him is an automatic laugh. The BBC clearly likes him too — he gives "field reports" on YouTube about how weird Earth is. And then he met Jago and Litefoot in a Big Finish audio story!
  • Brian Williams, Rory's Bumbling Dad. It helps he's played by Arthur Weasley.
  • Kate Stewart, because not only is she the Brig's daughter, she's a Badass scientist and quite the snarker. She even had the honor of being the first character from the revival to show up in the Big Finish 'verse in her very own UNIT based spinoff like her dad before her. To cap it off, she's played by Jemma Redgrave, who — perhaps unsurprisingly given that she is a Redgrave — waltzes away with every scene she is in. Like her dad before her, she has acted against most of the New Who Doctors: Ten, Eleven, Twelve, Thirteen, Fourteen and Fifteen.
    • Her right-hand woman Osgood, Genre Savvy Cosplaying Fangirl surrogate extraordinaire, is one in her own right, which led to a fan outrage when she was killed off in Series 8. She returned for Series 9 despite this, with the reveal that she and her Zygon double from "The Day of the Doctor" became "sisters", so there was still one around all along. Which one? She's not saying yet, and got to be the Doctor's temporary companion for a two-parter. Now she's in Big Finish too!
  • For "The Crimson Horror", despite being a parasite, Mr. Sweet actually won many viewers' hearts due to his cute name and face. In fact, when Ada kills him, some viewers were actually sad and wished the Doctor had saved him and returned him to his timeline.
  • The War Doctor is very popular even if he was only created exclusively for the 50th Anniversary — the fact he's played by Sir John Hurt no doubt helps also.
  • Journey Blue from "Into the Dalek". She proved to be so immensely popular after the episode's release that a not-insignificant number of fans have since been calling for her to become a companion — which is to say nothing of the people who took immediately to shipping her with Clara.
    • Rusty the good-not-good Dalek from the above episode. The fact that the scene featuring the character's death was removed from the final cut suggests the writers were aware of this.
  • Robin Hood from "Robot of Sherwood", due to his Large Ham tendencies and Hidden Depths at the end of the episode.
  • Adding to the list of Darkhorses provided by Series 8, there's both Psi and Saibra from "Time Heist".
  • The Curator who appeared at the end of "The Day of the Doctor" is extremely popular, and was voted as the best revival series guest star, largely due to being played by an elderly Tom Baker.
  • Perkins the train engineer from "Mummy On The Orient Express" is quite popular for his sharp mind and his witty tongue that can match the Doctor's. Many (including his actor, Frank Skinner) wished that he had accepted the Doctor's offer and became a companion.
  • Clara's sort-of companion Rigsy, from "Flatline" and "Face the Raven", has a fair few fans.
  • Yet another Twelfth Doctor companion who never was: lovable Shona from "Last Christmas", his first Christmas Episode. She and Journey were the most popular choices for his first post-Clara companion, but instead new characters were introduced, possibly because the circumstances of Clara's departure required a cleaner break from the past than usual.
  • Bonnie, the Zygon leader from "The Zygon Invasion"/"The Zygon Inversion", is loved by both fans and the cast. Her "Evil Clara" masquerade might just be Jenna Coleman's most popular character on the show, with even Clara haters taking a liking to her! And with her Heel–Face Turn turning her into the new Osgood "sister", Bonnie will have a special place in expanded universe media for years to come.
  • Erica, the botanist from "The Pyramid at the End of the World". She was widely noted as being far more likable and competent than Bill in that particular episode, and accordingly a lot of fans wished that she could become a companion at some point, taking up the Doctor's actual offer of such in-universe. Also very popular was the casting of dwarf actress Rachel Denning, despite the role as written having nothing requiring a non-average height. Alas, she became a case of What Happened to the Mouse? even though there was no reason the next episode ("The Lie of the Land"), which followed on from this episode's events, couldn't have included her if only to tie off the thread.
  • Grace, Ryan's grandmother and Graham's wife. Her loving nature and the fact that she immediately Jumped at the Call to help the Doctor defeat Tzim-Sha endeared her to many fans who naturally saw her as companion material, and were left brokenhearted when she gave her life trying to stop an alien monster from killing her grandson.
  • The Pting, the monster from "The Tsuranga Conundrum", became popular quickly due to both being adorable, like the Adipose, and people finding its "hangry" attitude to be very relatable.
  • Lin from "Resolution", an archaeologist who falls under the control of a Dalek she unearthed. Her well-developed romance with her partner on the job, nightmarish situation coupled with a killer performance as the Dalek takes control, and surprisingly living to tell the tale and perhaps even appear in future stories made her quite popular.
  • The Ruth!Doctor was an instant hit in the fandom, with some even saying they prefer her to the Thirteenth Doctor, or wanted Ruth!Doctor to be actually the Fourteenth Doctor, or having Jo Martin cast as the Fourteenth Doctor.
  • Jericho quickly became the most popular of the many new characters introduced during Flux due to Kevin McNally's performance. On top of the usual calls for him to become a proper companion, many criticized his dissatisfying death, with some viewers half-jokingly asking for him to be plucked out of time like Clara for further Expanded Universe adventures.
  • Ashad, the Lone Cyberman who debuted in The Haunting Of Villa Diodati became a fan favorite villain not long after his introduction, due to his unique design and subverting the Cybermen’s frequent defeat via The Power of Love by being a Cybermen without an inhibitor who wanted to be upgraded. Few were happy when The Master upstaged him in the Series 12 finale.

    Expanded Universe Debut 
  • 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.
  • The Dalek Time Controller from Big Finish Doctor Who is also becoming quite popular due to being a particularly cunning Dalek and The Chessmaster. A lot of people want him to appear on TV.
  • For an audio-only incarnation, Alex Macqueen's Master seems to have gained quite a vocal fanbase, some of whom wish to see his Master reprise his role on television.
  • Despite only appearing in one book, Engines of War, Cinder the Dalek Hunter has become quite popular, considering she gets killed off in that book. She was subsequently one of the first Expanded Universe characters to be incorporated into Doctor Who Legacy.
  • Of the many original characters introduced in the Doctor Who (Titan) lines, Time Surgeon — a punk Expy of the Twelfth Doctor who is the central character of an in-universe comic book and is Played for Laughs — may be the only one who has cosplayers in the real world.