- People have been asking "Doctor who?" since the very first episode (The Doctor himself delivers it when he is referred to as "Doctor Foreman"). It's been asked so many times that it's the oldest question, the one hidden in plain sight, which must never be answered, or silence will fall.
- Not to mention that anytime someone goes into the TARDIS for the first time, they have to say something along the lines of "It's bigger on the inside!"
- Darkly used by the astronauts' absolutely horrified reactions to it in "The Waters of Mars".
- Subverted in "The Three Doctors", when the Third Doctor asked Sergeant Benton why he hadn't said it yet, and Benton replied that it was obvious.
- Lampshaded in "Smith and Jones" when the Tenth Doctor mouths the words along with Martha, before saying, "Is it? I hadn't noticed."
- "The Vampires of Venice": Subverted when Rory first enters the TARDIS, as he correctly guesses that it's another dimension, to which the Doctor says, "I like the bit when someone says, 'It's bigger on the inside.'"
- Lampshaded in the audio drama Legend of the Cybermen, when a character enters the TARDIS, she is just about to finish delivering the line when both Jamie and Zoe in unison say "Yeah, yeah, we know..."
- Touchingly inverted by the TARDIS herself in "The Doctor's Wife", when the mind of the TARDIS inhabits a human body.Idris/The TARDIS: Are all people like this?
The Doctor: Like what?
Idris/The TARDIS: So much bigger on the inside...
- Inverted by Clara in "The Snowmen".Clara: It's smaller on the outside!
The Doctor: [taken aback] Okay... That is a first.
- Sent up in "The Husbands of River Song", when River doesn't recognize the Doctor's twelfth regeneration, she enters the TARDIS and tells him to prepare himself. The Doctor breaks into a huge grin and says "Finally, I get to have a go." He enters the TARDIS and goes on an epic, ham-filled rant about how his entire mathematical concept of space was just torn apart, then quietly says "I've always wanted to see it done properly."
- Another is the Doctor's complete inability to direct the TARDIS (though it's not so much their inability as the TARDIS's unwillingness to cooperate), so that they often step outside in full tour-guide mode only for the companion/s to point out that they are not, in fact, in Rome/Mars/Peladon/1980/Croydon/Rio.
- From the specially-shot Series 6 teaser for BBC America:
- One of the arcs/running gags of the entirety of Season 10 would be the Doctor's desire (and inability) to make it to Metebelis Three. Much of the first episode of "Carnival of Monsters" was spent with the Doctor obstinately believing he had arrived on the planet, and not on a cargo ship bound for Asia, circa 1926. The joke carried till "The Green Death" at the end of the season, when it became deadly serious for him.
- In the very earliest era, the First Doctor coming up with different mispronunciations of "Chesterton". This was broadened in some stories to aliens and non-English-speaking human characters having difficulty pronouncing "Ian". (Legend has it this started out with Doctor actor William Hartnell occasionally getting the name wrong during recording, to the point where it was adopted as a character tic.)
- Let's not forget that every time the Doctor regenerates, they spend a couple of minutes criticizing their new looks (Christopher Eccleston's ears, Matt Smith's chin, Jon Pertwee's nose...) As of the revival, they also complain they're STILL NOT GINGER!
- The phrase "You've redecorated! I don't like it!" is often used by the Doctor to criticize the TARDIS-theme of their successors. Also used by Eleven in "Closing Time" regarding Craig's house.
- Everything important in Time Lord society and culture is named after Rassilon; Time Lords also tend to invoke him (and the other Founders) the same way a human would when swearing by God. Gets a Lampshade Hanging in Big Finish, when the Doctor is tired of Rassilon's games:The Doctor: So what have you got squirrelled away [here]? The Hairdryer of Rassilon? The Hoover of Rassilon? The Rassilon Patent Trouser Press? "These creases last forever!"
- People unfamiliar with Gallifrey assuming it to be a place in Ireland. This happens in "The Hand of Fear", "The Invisible Enemy", the TV Movie and "Human Nature".
- Duggan breaking things or knocking people out in "City of Death".
- The continued references to running, though it might be Arc Words rather than this trope.
- In the new series, several of the Doctor's companions have encountered a prominent British writer under bizarre circumstances.
- In "The Unquiet Dead", the Doctor and Rose meet Charles Dickens on Christmas Eve and encounter ghost-like aliens.
- In "The Shakespeare Code", the Doctor, Martha and William Shakespeare meet aliens that resemble witches.
- In "The Unicorn and the Wasp", the Doctor and Donna help Agatha Christie solve a locked-room mystery (and Donna lampshades the situation, bringing up the Doctor's encounter with Dickens quite by accident).
- In "Victory of the Daleks", the Doctor, Amy and Winston Churchill save London from the Daleks (Churchill was not primarily known as a writer, but in his later years he did write a comprehensive history of World War II).
- This later carried over to the IDW Doctor Who comic book, where the Doctor and Rory meet Ian Fleming, and Rory (who was wearing a tux at the time) apparently inspires the creation of James Bond.
- "Harriet Jones, MP, Flydale North / (former) Prime Minister." "Yes, I know who you are." Even two types of genocidal alien baddies know her.
- The Doctor telling Jack to knock it off any time he says hello to anyone. Because when it comes to Jack, hello is never just hello.
- The first three Christmas specials of the new series ("The Christmas Invasion", "The Runaway Bride", "Voyage of the Damned") all involved aliens menacing present-day London, to the point that in the third one the city has been evacuated because the city's gotten wise to such things.
- The inability of the Tenth Doctor's companions to fake accents or modes of speech, and his pained reaction ("No. Don't... don't do that.") has been used four times; once in Season Two (Rose doing Scots), once in Season Three (Martha doing Elizabethan English), once in the animated special (Martha doing pirate talk), and once in the fourth season (when Donna Noble attempts to blend in at a 1920s upper-class party). The Doctor being horrified by Rose's attempts at a Scottish accent in the Season 2 episode "Tooth and Claw" is also a slight reference to the fact that Tennant himself is Scottish.
- This gag is nicely subverted in "Midnight", where, after suffering a traumatizing experience with a monster that mimicked and eventually stole his speech, the Doctor tells Donna "Don't. Don't do that" with DEAD seriousness when she repeats one of his catchphrases.
- The Tenth Doctor's season finales have a habit of ending with the Doctor sulking after his companion has left, only for something completely unexpected to appear in the TARDIS, ruining the moment and setting up the next episode. Heartbreakingly averted in "Journey's End", which ends with the Doctor in the TARDIS, sopping wet, reeling with the loss of Donna. Nothing else happens.
- Doctor Donna. Not a couple.
- References to UNIT-related incidents happening in the 1970s, "Or maybe the 80s" (and variants thereof). This is due to the fact the original 1963-89 series was inconsistent as to in what decade the earth-based UNIT stories of the Patrick Troughton, Jon Pertwee and Tom Baker eras actually took place. This uncertainty has since been incorporated into the show itself.
- On the subject of UNIT, The Brigadier was often stuck in Peru whenever he was needed.
- "The Waters of Mars":
- The Doctor keeps commenting that the base should have bikes so people can get around it faster, a Lampshade Hanging on the large amount of running in the show.
- The Doctor keeps saying that he should really go. This one eventually stops being funny.
- "Hello, sweetie!" Hi, River Song!
- Another one related to River that may or may not develop. Every time the Doctor finds a hat, he'll say "It's a(n) X. Xs are cool," and River will shoot it (often right off his head.) It's happened with the poor fez, and in the preview for Series 6, it happened to a Stetson.
- Series 5 adds the Eleventh Doctor's insistence that "Bowties are cool".
- Eleven likes hats, and obtains one whenever he can. Especially a fez.
- Even that was a reference to the Seventh Doctor serial "Silver Nemesis".
- Back even further, at the very beginning of the Second Doctor's era he wore a tall funny hat, and his catch-phrase was "I should like a hat like that" whenever he saw someone with interesting headgear. Sadly (or perhaps not), most of these stories were wiped, and the whole thing was forgotten. But add in the Fourth, Fifth, and Seventh Doctors' careful cultivation of their own special hats, and it's definitely a very long-running thing.
- Clara (and her echoes) and her inability to make soufflés. The running gag only survived until the end of phase 1 of her story arc at the end of Series 7 and was abandoned as the character matured.
- "The Woman Who Fell to Earth" has an episode-long running gag of the Doctor either lamenting that her pockets are empty, as she lost everything in them when she fell out of the TARDIS, or having trouble finding things in her pockets because she's still wearing Twelve's clothing, which is a bit too big for her.
- "Arachnids in the UK": Najia Khan is constantly correcting people on her name. Corrupt Corporate Executive Robertson keeps calling her "Nadia", and the Doctor calls her "Yaz's mum".
Running Gag / Doctor Who