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For a series that was originally conceived at least partly Edutainment series for a family audience, Doctor Who, especially in the new series, has snuck a few past the TV code (for the most part, these are from the 2005-present revival series; the original 1963-89 series tended to attract more concern about violence than innuendo).
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The Hartnell Years
The Hartnell Years could give the new series a run for its money in the sex department:
In "An Unearthly Child", Ian suspects Susan might be sneaking into the Junkyard to "see a boy" (innocent enough out of context, but bear in mind she's sneaking into an abandoned Junkyard in the middle of the night, suggesting that Ian thinks she's got more than holding hands in mind).
A jailer in "The Reign of Terror" pretty much offers to let Barbara go in return for sex. Thankfully she doesn't oblige.
Barbara was almost raped again in "The Romans", this time by Emperor Nero.
In "The Chase", Ian is implied to habitually engage in some rather conservative crossdressing:
Ian: Oh, er, Barbara, could, I, er, have your cardigan?
Barbara: Oh, not again.
Ian: It's for the Dalek, not for me.
Edith is strongly implied to be gang-raped off-screen by the three Norwegian scouts in "The Time Meddler", as confirmed by Verity Lambert on the DVD commentary. She also explains why the Hartnell era had a higher concentration of sex references; though social taboos were stricter due to the recent introduction of TV, there was less in the way of strict rules on content. In general, there was a tacit understanding of what was appropriate for broadcast, but whether a specific sequence breached it or not was mostly a matter for the personal opinion of the producer.
This little gem from "The Myth Makers": "Upon my soul, you're making me as nervous as a Baccante at her first orgy." Steven Moffat at least tries to disguise his dirty jokes.
"The Celestial Toymaker" includes The King of Hearts reciting a very offensive version of Eeny Meeny Miny Moe. That slipped past the censors in the UK but American networks wouldn't play it.
The (intentional) Ho Yay between the Second Doctor and Jamie is fairly tame by today's standards, but pretty extreme considering homosexuality was illegal at the time (although decriminalised). Some is actually fairly clear by today's standards - like the Second Doctor fondling Jamie's sporran, or looking up his kilt when he's standing on the Doctor's shoulders (preserved only in telesnap form, sadly).
"The Dominators" has a part where Jamie climbs a ladder to open a grate - if you pay attention to Cully standing at the bottom, he looks up at the grate, suddenly realises he can see up Jamie's kilt, and has a sudden surprised and appreciative reaction.
The Pertwee Years
Doctor Who is classified as a children's/family show. "The Time Monster" has the Master on Earth making a teleporter that pushes matter through time and space called "Transmission of Matter Through Insterstitial Time". They even use the abbreviation TOMTITnote This is a kind of cute little Australian bird.. One investor gets mad at the expense and that the machine doesn't seem to work properly. "Even the name is offensive! TOMTIT", with an emphasis on the last three letters. And STILL nobody in the censor board noticed.
It's also Cockney rhyming slang for, well, exactly what you think.
The Tom Baker Years
"Robot" has an Oedipus Complex theme, backed up by Phallic Weapon and Compensating for Something visuals. For instance, after killing his "father," the robot collapses outside of the rather yonic base door with the disintegrator (a large gun with a pink tip) lying on its groin, and the Brigadier touches it. Later, after the Doctor explains to Harry about Freudian psychology and "compensation," we see the Brigadier about to fire the disintegrator from the hip in an extended and very phallic shot.
Sarah Jane has a scene where she's trying to charm her way past the Brigadier by flirting with him. When he reminds her that he's married by talking about dancing she tells him, "oh, nonsense, Brigadier, you're a swinger!" Made even more blatant by the new series using 'dancing' as a metaphor for sex on several occasions.
"The Talons of Weng-Chiang" has a bit of fun with Victorian Have a Gay Old Time when Litefoot finds and plays with a phallic object in Greel's carpet bag and Jago exclaims, "What a queer collection of objects!"
When Tom Baker appeared in-character on Swap Shop (in a special feature available on the "The Hand of Fear" DVD), he managed to sneak one in while being interviewed by a caller who kept stammering:
Child: How big... how long... how big is your...!
Tom Baker: (glances up towards the camera with a shocked and offended expression)
"The Stones of Blood" has one half of the Les Yay-laden guest character double act make a suggestive remark to Romana about how much fun she can have with a bicycle seat.
"The Creature From The Pit":
There is a genuinely unintentional Unfortunate Character Design for the monster, which turned out to resemble a giant green cock-and-balls, to the costume department's horror and to Tom Baker's great amusement. He spends several scenes miming masturbation or fellatio on the thing, reads his lines about the monster with facial expressions and emphasis to make them into dick jokes, and that's before you get into Romana's scripted BDSM jokes about her relationship with the Doctor.
Forget her relationship with the Doctor; Romana spends half the serial being tied up, interrogated, slapped across the face and claimed as a 'handmaiden' by a woman in red-and-black leather who calls her "my dear" and seems to enjoy manhandling her whenever possible.
The Creature, looking exactly like a dong, being named "Erato" - a few letters away from "erotic" and the name of the Muse of pornography. Tom Baker rubs his mouth and licks his lips a lot while talking to it.
Camilla in "State of Decay" is a pretty obvious Lesbian Vampire and molests Romana.
In "The Two Doctors", Peri mouths "you asshole!" at the villain, although nothing can be heard.
In "Revelation of the Daleks", there's a dialogue between the Doctor and Peri after he helps her climb over a wall which seems to imply that she accidentally kicked him in the genitals and did some permanent damage. It's revealed at the end that he's complaining about a broken pocket watch.
The Eccleston Years
"The Doctor Dances": the Doctor discusses "dancing" with Rose, a little miffed that she assumed he'd never "danced" before. He has, it's just been a while. Later, when the Doctor and Rose are dancing note the literal kind of dancing in front of Jack, Rose assumes that Jack wants to cut in and dance with her. As it turns out, he'd rather "dance" with the Doctor.
"Dalek": Viewers were apparently so upset over a reference (in a sexual context) to "spooning" (lodging a number of complaints) they appeared to miss the fact one of the characters in this episode utters the strong (even for 2005) swear word "goddamn," which as of 2013 remains the strongest word uttered in the main Doctor Who series (for stronger language, you need to watch Torchwood). That may be dependent on your location — in the UK and in Australia, neither "damn" nor "goddamn" are really considered swearwords.
Cassandra: She's back! Oh, that little blonde bi— [cut to the Doctor and Rose talking] Rose: Bit rich, coming from you. [...] Cassandra: That portion of skin came from the front of my body. This... came from the back. Rose: Right, so you're literally talking out of your ar— Cassandra: Ask not. [...] Cassandra:[in the Doctor's body] I'm a man! So many parts... and hardly used. [significant look at Rose]
In "Love & Monsters", Ursula gets reduced to a face in a pavingstone. Elton remarks that they "still have a bit of a love life."
In the mini-special "Time Crash", The Tenth Doctor mentions to the Fifth Doctor (their TARDISes intersected when Ten was redecorating) that the Master is running about again. Five asks whether or not the Master "still [has] that rubbish beard." Ten responds that no, but he does have a wife.
The 1920s porn that Colonel Curbishley secretly looks at in "The Unicorn and the Wasp." That got more questions from the kids than the gay relationship in the episode.
The Matt Smith Years
"The Eleventh Hour" has The Doctor run into a man he met earlier to use his laptop. When he snatches the computer away and looks at it he says "Blimey! Get a girlfriend!"—and later on: "Delete your internet history." Bravo Moff.
And in "Flesh and Stone", there's the scene in Amy's bedroom. How the hell did they get away with that?!
There is a hilarious example in "The Vampires of Venice", in which Rory pulls out a tiny light with which to ward off the vampires. In response, the Doctor immediately pulls out a massive ultraviolet bar.
Rory: Yours is bigger than mine. The Doctor: Let's not go there.
"Oooh, Doctor, you sonicked her..." To make this even more remarkable, that's her daughter she's talking about. Although she and the audience don't know that yet.
And in "Vincent and the Doctor" the monster seems to rather enjoy one of the sonic settings. The monster even returns the favor by repeatedly bumping a door that Eleven is leaning against. Eleven has a visible reaction.
In "A Christmas Carol", Amy and Rory are wearing their policewoman and Roman costume throughout the whole episode (having just had their honeymoon interrupted), and always change the subject when someone brings their clothes up.
Rory: You know, history lesson, a bit of fun every now and then, a bit of nostalgia!
Rory: Heh... no. Why do I get slapped? The Doctor: Because we have to stick to the established chain of events. One mistake and the whole timeline could collapse. We'd end up with two Amy Ponds forever, and then what would you do? [Rory looks at Amy with raised eyebrows] Amy:[gasp; slap]
The Doctor:[regarding his and River's destination] You could read a book by [the stars]. River:[suggestively] Is it okay if I don't? The Doctor: We've got ten minutes, so get dressed. River: Oh, that's so close to the perfect sentence. The Doctor: Hmm.
A bit later...
The Doctor:[referring to the diary] From now on, there are rules. River: Ooh, Doctor, you've got all strict — not that I mind.
From "Last Night":
[The Doctor is trying to resuscitate a Future!River, who's playing dead] The Doctor: River... you are holding your breath. River: You're a fine one to talk about holding. How many hands do you have?
The Doctor: River, you can't do things like that! River: Or what? [...] What else are you gonna do, spank me?
[yet another River enters the TARDIS, followed by her Doctor] Future!River:[sees Present!Doctor] Two of you! The mindraces, does it not? [Future!River and Future!Doctor leave, just as Present!River returns] Present!River:[seeing Future!Doctor] Two of you! The mindraces, does it not?
With none of this taking into account a certain dress.
In the 2011 Christmas Special "The Doctor, the Widow, and the Wardrobe", there is a scene where, in order to save a planet full of sentient alien trees, the title widow, Madge, takes the collective "souls" of the trees inside herself. During this process, she seems to be having an orgasm.
The Series 6 trailer has a naked River, though anything cleavage-based isn't seen. The scene was cut from the final episode.
"Handcuffs! Why do you always have handcuffs?" Followed by "You. Me. Handcuffs. Must it always end this way?"
The Doctor: I don't know, but I can't feel my feet... And other parts. Rory: I think all my parts are basically fine. The Doctor: Stop competing.
Also in that episode, the Dream Lord says to Amy "The Doctor left you alone with me. Anything can happen." And as he says those last two lines he transforms into wearing basically a bathrobe and has a very creepy expression on his face.
"Asylum of the Daleks" has, at the end of the episode, Amy and Rory—their relationship repaired—standing outside their house. Amy gives Rory a steamy look and walks inside. He smiles for a second, fist pumps * ('''Amy:''' "I can see you!"), and follows her.
"Pond Life" part two has one combined with a noodle incident—the Doctor bursts into Amy and Rory's bedroom, only to immediately cover his eyes and yell at them to "stop what [they're] doing!" They were only sleeping, but considering they also have a rule about the Doctor bursting into the bedroom...
Amy is probably wearing either a bra or lingerie under the sheets, as she's clearly hiding her breasts while Rory allows his plain, blue T-shirt to be seen.
Also, at the end, Rory says, "I really hate it when he does that," suggesting that the Doctor has walked in on them more than once.
Melody Malone and her "cleavage that could fell an ox at twenty feet." The Doctor's clearly enjoying himself reading too, given the "Yowza!" It's really not so bad considering it's River Song and therefore his wife. On the other hand, he's reading it in front of her mother, and River herself wrote it.
According to the behind-the-scenes publication The Doctor Who Companion: The Eleventh Doctor Vol. 6, the original script would have had the Doctor utter the phrase "Traffic was a bitch." Evidently either Steven Moffat or the powers that be thought better of this and changed the dialogue.
River has a subtle Showing Off the New Body moment in "Let's Kill Hitler" when she walks offscreen for a few seconds to (it's heavily implied) check out her new body's butt in a mirror. We only hear her shrieking in delight, and later promising that she's "going to wear lots of jodhpurs!" Because it happens offscreen, it's not blatant enough to count as outright Fanservice. Also, the joke is only obvious if you know what jodhpurs are. Even moreso, when you consider that she's wearing a loose-fitting dress in that scene—meaning that she'd have to have deliberately lifted up her dress to get a good look at her bottom. Which would be way too saucy to show on-screen on an episode of Doctor Who.
The made-for-DVD minisode "Clara and the TARDIS" has Clara conducting a surprisingly frank conversation with the TARDIS about whether she's the first girl the Doctor has had, ahem, stay the night. The TARDIS's subsequent slideshow of past female companions (with Clara taking particular notice of Amy's legs) leaves it unclear—from Clara's point of view—as to whether or not these were actually past romances of the Doctor. To her credit, she seems to take this lengthy "girlfriends list" in stride. One wonders about her reaction had the TARDIS chosen to also display images of Adric, Harry Sullivan, or Captain Jack. A virtually identical gag is used in an Amy minisode where she makes the TARDIS display images of the former companions, taunts the Doctor about it, and gets a Head-Tiltingly Kinky reaction to a woman in a "leather bikini" (a reference to Fourth Doctor Nubile Savage companion Leela).
The Capaldi Years
Strax checks Clara's subconscious and finds "Muscular young men doing sport," then adds the clarification that it "could be called 'sport' ". Someone's a Yaoi Fangirl. (Or a Yuri Fan, if he's again mixing up the genders.)
Another in that episode: Clara kicks the sonic screwdriver up into the doctor's lap and he makes a face.
Clara: Sorry, did I... hit something?
The Doctor: Oh, the symbolism.
"Robot of Sherwood" has the Doctor doubting if Robin Hood is real or a sham. Looking for biological proof, he gives each of Robin Hood's Merry Men an intrusive examination, and saves the most intrusive one of all for Robin Hood himself. The Doctor approaches Robin Hood with a goblet—at crotch level... suggesting he was going for a urine sample.
Not to mention Mark Gatiss wrote the episode, and his trademark use of campy innuendo shows. The scenes where Robin Hood and the Doctor argue are rife with attempts by each to one up the size of each other's manly pride, among other things.
Plus the freeze-frame bonus as The Doctor is putting his gauntlet on. His facial expression and finger positioning are most eloquent.