In "The Macra Terror", the Macra freak out when the Doctor has the Pilot on his side and is about to use the gas from their lifeline to blow them all to Kingdom Come.
In part six of "The Enemy of the World", Giles Kent and Ramón Salamander are going into the so-called "records room", and Kent thinks Salamander is demonstrating Obfuscating Stupidity as regards an explosives room they had devised long before their falling-out. Kent reminds him of this room and then Salamander reveals that he is not Salamander but the Doctor. Kent is understandably perturbed — the Doctor is not supposed to know of their past connection.
In "Inferno", the Third Doctor gets one whern he is about to leave UNIT with the TARDIS console. Before he goes, he tells off Brigadier Lethbridge-Stewart in no uncertain terms. Then, he rematerializes... in the garbage heap next door, realizing that an irate Brig is within earshot...
Another Dalek example, from "Day of the Daleks". It turns out that Jo (who's been captured) wasn't working on her own:
Controller: The girl referred to a companion in her own time zone. She called him... "the Doctor". Dalek:Doc-tor? Did you say "Doc-tor"?!
From "Robot": "You let Sarah go somewhere with Kettlewell?"
"The Invasion of Time" is the definitive Classic Who example. After four episodes, the Vardans have been expelled from Gallifrey through copious amounts of mind-trickery; the Doctor, supremely smug with his success, addresses the cheering crowd with a victory speech. Puzzled at why the cheering abruptly stops, he turns around... and standing behind him is a Sontaran battle squad, who have been playing the Vardans for patsies, and have taken advantage of the weakened Gallifrey defences to stroll in and claim the place for themselves. Tom Baker's boggle-eyes were MADE for moments like this.
In the final part of "Trial of a Time Lord" when the Master reveals that the Valeyard is actually the embodiment of the Doctor's dark side, taken from a point after his twelfth incarnation. The look on the Doctor's face shows he knows full well what he's capable of—and this is long before the final events of the Time War.
The Doctor is always good for one of these. At the end of the first episode of the serial, in which the Doctor and Ace flee from a Dalek by going up the stairs, because Daleks can't climb stairs. Except, no, this one can.
And just before that:
Ace: The operator? The Doctor: Yes, the Daleks usually leave an operator on station in case of any malfunctions. Ace: ...and that would be another Dalek? The Doctor: Yes...
Mr. Parsonsnote who was actually Ian and Barbara's old boss just has time for a Big "NO!" when the Imperial Daleks kill him as a security risk.
Mr. Ratcliffe has one when the Daleks reveal that they had played him like a violin and they never had any intention of sharing power with him.
Doctor Who New Adventures time — The Dying Days apparently kills off the Doctor within the first third of the story. Then the villain of the piece has been tricked into ranting about his plans by the Doctor's companion despite knowing full well that doing so would offend his "honour" to the point of him executing her on the spot. She gets ready for the chop when a quiet voice says "it ends now", it's a full blown "oh crap" and "hell yeah" moment - as eventually the speaker reveals themselves, and you guessed it, it's the Doctor. Who is happily aboard the villain's ship and is merrily messing with everyone's plans. The stunned silence on everyone's behalf speaks volumes.
In A Fix with Sontarans, when the Doctor and Tegan see Jimmy Saville on the viewscreen. Of course, neither the screenwriter nor the actors knew the real reason Six and Tegan had the reaction they did...
The Doctor has Oh Crap moments often enough that the TARDIS has a standard signal for them, the Cloister Bell. But only for very specialOh Crap moments. The TARDIS rings it when she detects that the universe is coming to an end.
When Rose believes they have escaped the Dalek by running up a flight of stairs. Adam mocks it and the soldier orders it to return to its cell. One word: "Elevate:"
The actual reveal of the Dalek to begin with. For the Doctor, it's the first clue that the genocide that ended the Time War wasn't as complete as he thought it to be.
The Doctor: Look, I know Mr. Van Statten might think he's clever, but never mind him. I've come to help. I'm the Doctor. Dalek:Doc...tor? Nine:Impossible...! Dalek:THE Doctor?! (as the Dalek is revealed) Dalek:EXTERMINATE! EXTERMINATE!EX-TER-MI-NAAAAAAAATE!
"Father's Day": The (Ninth) Doctor and Rose have just had a falling out, and he goes back to the TARDIS, to give both of them time to cool off. He opens up his little blue police box to find... it's a police box. Cue beat of sheer horror, followed by running back as fast as he can.
The Doctor has a Crowning Moment Of Awesome when he defeats a child-led zombie invasion by sending the child to his room. When the Doctor investigate a private hospital's records of the child's death, they uncover a recorded interview with him and a Room Full of Crazy zombie-child drawings. The Oh Crap moment? The realization that the taped interview ran out, and the child's voice is live, because the Doctor sent him to his room. This room.
The moment with the typewriter. A small boy wants to do some typing, so he does. Nothing scary about that... until Nancy mentions the fact that he stopped typing a minute ago, but the typing was still going on. Not to mention that what was being typed was "Are you my mummy?" over and over.
From the episode "Bad Wolf": the Doctor brings down the masking signal hiding the true force behind Satellite 5, revealing a Dalek ship. Then the camera pulls back to reveal dozens upon dozens of them. The Doctor's face says it all. And then it gets turned around in a Crowning Moment of Awesome, when the Doctor announces exactly what he's going to do about the situation:
The Doctor: 'Cause this is what I'm going to do: I'm going to rescue her! I'm going to save Rose Tyler from the middle of the Dalek fleet! And then I'm going to save the Earth! And then, just to finish off, I'm going to wipe every last stinking Dalek out of the sky! Daleks:But you have no weapons, no defences, no plan! The Doctor: Yeah, and doesn't that just scare you to death?
It continues to go back and forth in the opening scenes of "The Parting of the Ways": first the Doctor confronts the Daleks: "I'm the Doctor, and if there's one thing I can do it's talk! I've got five billion languages and you've got no way of stopping me, so if anybody's gonna shut up, IT'S YOU!!" — and a Dalek actually recoils. Then, seconds later, the God of All Daleks declares, "These words are blasphemy!" — the look on the Doctor's face as he realizes that the Daleks have found religion...
There's a similar one near the begining of "The Girl in the Fireplace", where the Doctor realises that the clock's broken — so what's ticking?
At the cliffhanger of "Rise of the Cybermen", the Doctor gets a good one when he realises the Cybermen aren't going to let them surrender.
In "Night Terrors", the moment when the Doctor gets Alex to realize that George can't possibly be his son because Claire, his wife, can't have children. Cue look of horror on Alex's face — if he doesn't have a son, then who and WHAT is the child that's been living with him for ten years?
The Daleks manage to provoke this expression twice in "Army of Ghosts" while having approximately ten seconds of screen time. First, the Doctor's face screams "Oh shit!" when the Cybermen tell him the Void Ship isn't theirs, then, when they actually appear, it's Rose's turn.
Lacking faces, you wouldn't imagine the Daleks could pull off a decent Oh Crap moment. But in "Doomsday", when a strange man shows up on the vidscreen the Daleks are watching (and have just informed five million Cybermen that they are no threat, claiming that destroying them "is not war, this is pest control") and they demand Rose identify him, she calmly does so: "That's the Doctor." All four Daleks simultaneously jerk a few inches backwards. Rose's line is priceless:
Rose: Five million Cybermen, no problem. One Doctor... now you're scared.
The Master is unimpressed with Martha's speech in "Last of the Time Lords" until she ends with "... but with 15 satellites." The resulting "What?" could easily have been an "Oh shit" if this weren't a family show.
"Midnight". Sweet holy hell, "Midnight". When the Doctor is taken over by the Midnight Creature and Sky is convincing the rest of the passengers to throw him to his death, confirming the Humans Are the Real Monsters that he's been trying desperately to avert all episode, the look on his face has to be seen to be believed. Super Bonus points to David Tennant for distilling all of the Doctor's thoughts into just his face, considering he was in a state of Mind Rape and couldn't move or speak in his own voice. Of course, part of the Mind Rape was that he couldn't really move his face either, so he was stuck with an Oh Crap expression the entire time. It's the eyes that made the scene.
Donna is exposed to an alternate reality in which she never met The Doctor, causing the events of "The Runaway Bride" to end with him dying and everything to be a dystopia. When she breaks free and returns to the normal reality the Doctor comments that she's brilliant and she suddenly remembers that a woman (Rose Tyler) from the other reality said that he had said that about her. Then she remembers what she said to her just before she "dies".
Donna: No, but she said it was all worlds. Every world. She said the Darkness is coming. Even here. The Doctor: Who was she? Donna: I don't know. The Doctor: What did she look like? Donna: She was... blonde. The Doctor: What was her name? Donna: I don't know. The Doctor: Donna, what was her name? Donna: But she told me to warn you. She said two words. The Doctor: What two words? What were they? What did she say? Donna:"Bad Wolf." What does it mean? Doctor, what is it? What's "Bad Wolf"?
His face at the mention of the Arc Words is a look of sudden realization and an Oh Crap as he responds with;
The Doctor: It's the end of the universe.
In the very same episode, as Rose Tyler and Donna Noble get ready to send Donna back in time:
Rose: Good luck. Donna: I'm ready. Rose: One minute past ten. Donna: 'Cause I understand now. You said I was gonna die, but... you mean this whole world. It's gonna blink out of existence. But that's not dying, 'cause a better world takes its place. The Doctor's World! And I'm still alive! (Rose doesn't answer) Donna: That's right. Isn't it? I don't die, if I change things, I don't die, that's... that's right, isn't it? (Rose remains silent until...) Rose: I'm sorry.
The look on just about everybody's face, (especially Captain Jack's) when they realize it's the Daleks, and they're coming this way!
For her part, Sarah Jane actually wobbles as if her legs are about to give out. And then again when Davros reveals himself.
The Doctor gets one too when he finds out in that not only is Davros still alive, he's made an new army of Daleks, numbering millions.
And then there's the look on Davros's face when Dalek Caan says "No more". This is likely because Dalek Caan has done the one thing that Davros had specifically designed the Daleks to NEVER be capable of: Dalek Caan repented.
(the Doctor is searching through a house) >The Doctor: There's one more thing I cannot figure. If this room's got infostamps, then maybe, just maybe, it's got something that needs infostamping... (he opens a door and finds a Cyberman; he closes it again) OK... I think we should run.
During the Hope Spot, the Doctor thinks he's cheated death, thinking the Master or the Time Lords were going to kill him... and then he hears Wilfred *knock-knock-knock-knock*ing to be let out of a booth that's going to flood with radiation. The look on his face when he realises it is absolutely heartbreaking.
Only fair, given the moment he gave the Doctor earlier.
The Master: Oh that's too simple... no no no no no. They're not going to think like me... ...They're going to BECOME me!
There's also the Doctor's reaction when he realizes that the Time Lords are returning. David Tennant really sells it in that scene.
Also, how about Lucy Saxon's reaction when she realizes that the prison she is in is staffed by members of a crazed cult hell-bent on using her to bring back the Master. Keep in mind, The Master's Mind Rape has worn off and this is the same man she shot two years earlier because she was scared to death of him.
"The Eleventh Hour": Latest on the alien "Oh, crap, it's him" list is the Atraxi. After the 11th Doctor dresses them down for planning to destroy the Earth just to get an escaped prisoner, he asks them if they think the planet is under protection. Flash to a hologram showing Cybermen, Daleks, the numerous other aliens who have tried to conquer or destroy the Earth, and then a sequence showing every incarnation of the Doctor, ending with the latest walking through the hologram with a cheerful "Hello. I'm the Doctor." The Atraxi leave very quickly. Even more impressive with this is that the Atraxi are giant EYEBALLS, and still manage a complete and total "oh crap" expression.
"The Time of Angels": Whilst hunting a Weeping Angel in a six-story temple full of statues, it dawns on the Doctor that...
The Doctor:If [the race that built this place] had two heads, then why don't the statues?
And this is why, when River Song managed to give A GODDAMN DALEK an Oh Crap moment, it was terrifying. To elaborate: in 'The Big Bang' the Daleks have made the rather stupid mistake of shooting the Doctor. River assumes him dead, but the half-resurrected Dalek's guns aren't at full power. River encounters the Dalek responsible, levels her gun at him and coolly promises to shoot him right through the eyestalk. The Dalek remarks that she is an associate of the Doctor; records indicate she will show mercy. Cue River giving the Dalek the evil eye and growling, "I'm River Song. Check your records again."
Dalek:Mercy. River: Say it again. Dalek:Mercy! River: One. More. Time. Dalek:MERCYYY!!!
You can tell the Dalek's fear is going up with each iteration of "Mercy", despite being mostly monotonous. It goes from "Oh Crap" to "Please don't kill me!" to "DEAR DAVROS I'M GONNA DIE!!!"
Turns out there's a very good reason for why it was so afraid. Series 6 reveals that River is the person history records as (supposedly) doing the one thing they never could; Kill the Doctor!
The Doctor has accrued such a reputation by now that many aliens see him as a mythological figure, causing many an Oh Crap when he introduces himself. Perhaps the greatest is that of the Vashta Nerada, made all the more impressive by the fact that they can express it whilst being a shadow on the floor. "Look me up." Indeed.
Slightly earlier in the same episode, the Doctor's reaction when River tells him the date she's been dragged to the 26th of June 2010, otherwise known as the date the TARDIS explodes. The look on his face, and the way his voice softens for an instant as he tells her to "Get out of there now," is a suitable indicator of how real shit just got.
And even before that River has one when she realises (from investigating Amy's bedroom) that the whole scenario in 102 A.D. is a trap for the Doctor, constructed from bits and pieces of Amy's past.
River gets a great escalating Oh Crap moment when her scanner shows the ten thousand-plus battleships in orbit around Earth. Alex Kingston does a terrific job of showing the rising Oh Crap-ness of the situation.
An example even earlier in the episode (really the whole thing is one series of "Oh Crap" moments), when the Doctor realizes that Stonehenge is broadcasting throughout the universe that the Pandorica is opening, and just who might be coming to their exact location (Daleks, Cybermen, etc.) His reaction: "Oh..."
There's a great one that's mostly played for laughs:
The Doctor: (reclining at the president's desk) Fellas, the guns? Really? I just walked into the highest security office in the United States, parked a big blue box on the rug. You think you can just shoot me? River: (bursting out of the TARDIS, screaming) They're Americans! The Doctor: (suddenly very frightened) Don't shoot! Definitely no shooting!
Amy and the Doctor get a shared one in the cliffhanger ending. Canton is unconscious, and a familiar, ominous astronaut is slowly approaching. Amy, recognising the space suit as that worn by the killer of the future Doctor in 2011, grabs Canton's revolver and gets ready to shoot, hoping to prevent the Doctor's demise. But while she's facing the other way to load the gun, the spaceman lifts its visor to reveal the pleading face of a little girl, which Amy doesn't notice until it's too late. Screaming, she whirls around and fires a single shot. Both her and the Doctor's faces when they realise what has happened embody the heck out of this trope.
In the second part, the Doctor engineers the Silence to order their own genocide. Canton filmed a downed Silent saying "You should kill us all on sight" and splices it into the moon landing LIVE. The Doctor sums it up perfectly with "I think the word you're looking for right now is 'Oops'."
From the same episode, there are multiple Oh Crap moments involving the Silence: Any time someone's hand starts blinking red, indicating that they've seen a Silent but can't remember it; and the black tally marks on the characters' arms, which serve the same purpose. Amy gets a particularly effective one when she's looking for the little girl in the orphanage. She catches a glimpse of her reflection in a window, only to find that suddenly there are tally marks ALL OVER HER FACE. Then she slowly looks up...
It's revealed that River Song is Amy's daughter, only from the future. Given what he and River got up to the last time they met, that Amy and Rory are standing right there when River tells him, and that Rory has a sword, it proves to be something of an Oh Crap moment for the Eleventh Doctor.
The Doctor can be heard speaking: "Imagine you were dying and a long way from home and in terrible pain. And just when you think it couldn't get any worse, you look up and see the face of the devil himself." And then we see who he's addressing: a Dalek. Who immediately starts screaming "EMERGENCY! EMERGENCY!"
And those who had an Oh Crap over Ten going Time Lord Victorious will have an all-too-familiar reaction to Eleven's last words to the Dalek he murders, in the most cold sociopathic voice he has ever used: Hello... Dalek.
A much more pleasant one comes when Madame Kovarian realises Amy is about to give full vent to her Mama Bear fury when the Doctor isn't there to stop her, and really is going to kill her.
"I was going to get coffee for the Doctor and Amy. Hello, River."
In "The Name of the Doctor", Eleven gets a big one of these right after a heartwarming reunion with Clara. The actual cause is kind of a massive spoiler, however: It's the memory of the one Doctor that the rest of the regenerations refuse to acknowledge as such.
The Daleks boast victory at the dying Doctor when they acknowledge that he has run out of regenerations. Until he gets a gift for Christmas — namely a new regeneration cycle from the Time Lords. They completely freak out when he fires up the first of them immediately... and he whips up enough energy that he can use it to destroy them.
Supreme Dalek:EMERGENCY! EMERGENCY!! THE DOCTOR IS REGENERATING!! THE DOCTOR IS REGENERATING!!!
Clara has two in a row at the end of the episode: The first one is her priceless reaction to her beloved Time Lord regenerating from the Eleventh to Twelfth Doctor and becoming vastly different, older, and quite scary at first glance... 'til he starts babbling about new kidneys. The second one really packs a kick. There's one big problem with the Twelfth Doctor just as the TARDIS starts crashing out of control: the regeneration has made him forget how to fly the TARDIS. Clara is terrified.