The whole Orieni Empire had one when they learned the Centauri have just invented the mass driver, the setting's way to deliver a Colony Drop. Given what happens when the Centauri finally drive back the Orieni and invade their space, it's Justified. Even if the first hint of the mass driver's existence hadn't been a world having its geography rearranged.
Also, the ship discovering of its existence has a massive one when they do, because they also realize the Centauri ship mounting that weapon is aiming it at them.
A common reaction to a great many things in Tiberium Wars. For example, GDI troops have a spazzing panic attack whenever they encounter the Black Hand (for good reason), and the Nod troops have one when they encounter an entire division of Mammoth Tanks.
When The Burning Talon's laser destroys the gates of Cloudsdale in chapter 8, Lightning Bolt, Derpy and Soarin' just stare at it for a while, realizing they are screwed.
Ironic Echo: the griffins have the same reactions two chapters later when said superweapon is destroyed.
Firefly has this moment when she realizes Scythe is about to perform a Suicide Attack as he tries to bomb Stalliongrad.
Red Cyclone gets a glorious moment when Firefly arrives to help Rainbow Dash in destroying Fortress Intimidation.
During the Avatar Island arc of Dungeon Keeper Ami, Mercury defeats and kills the Keeper, Self-proclaimed 'Emperor' Zarekos, currently sole despot of the Avatar Islands. The Oh Crap moment comes in when Zarekos comes back as a Ghost. Considering the guy was a Dungeon Keeper, and the souls of Dungeon Keepers go to the Realms of the Dark Gods when they are killed or their Dungeon Hearts are destroyed, him coming back after having been physically killed is a major reversal moment. Of course, he was in the process of making himself a god prior to his physical death.
There are tons of examples in An Entry with a Bang!, starting with the initial pirate raid in 2005, when people on Earth realize that they're getting visited by what they thought was a purely fictional universe.
The Inner Sphere rediscovering the value of the TAG (Target Acquisition Gear) warning light, courtesy of Earth's laser guided munitions, also qualifies. Not that most of them survive the lesson, mind you...
The pirates get one when Earth starts firing nukes at their fleet.
There's a Mass "Oh, Crap!" moment in Chapter 19 and Chapter 24, both times after the heroes are reunited... just in time for the Spinosaurus to show up.
Another T-rex elicits this reaction from Violet, Helen, and Dash in Chapter 20, when they realize that it's smack in the middle of their campsite. From the same chapter, Vi gets a minor one when she discovers that Velociripper has found his way back to Isla Nublar.
Chapter 31: A bunch of mooks get this after messing with the wrong character, resulting in a Bring My Brown Pants moment. Helen puts it this way:
But then I noticed that the gang leader wasn't looking at me. His gaze was, very, very slowly, turning upwards. That was when we heard a snort behind us. I noticed that I'd been backed into the rock in the middle of the clearing.
Chapter 35: First Sarah, then Adam let out an anguished Big Word Shout when they think that Violet has been killed off. And in the end, Ludlow lets out "a long, loud, high-pitched, piercing scream of complete and absolute terror" before and while he really iskilled off.
The Princesses when they begin to realize what they're dealing with.
Twilight, doing research into what's happening, finds references to the "Messenger of the Old Ones" and its multiple titles, including "Herald of the Outer Gods"... and realizes that the stranger she's alone with just introduced himself as "Herald".
In The Prayer Warriors, Ron's reaction after he realizes that Harry Potter has been killed and his key has been stolen by the Prayer Warriors is to fall "to his feet" in shock, immediately before Ebonynote not the My Immortal Ebony kills him.
In The Boy With The Magic Notebook, The Undersiders thought they were in deep trouble when they thought they heard that Dragon had arrived at the PRT headquarters during their raid. However, Lily's giggling meant that she knew it was really her brother Maxwell. Which was actually worse.
Regent: Yeah that’s nice, only it’s not Dragon. I said a dragon. I’m talking about a fire breathing, laser shooting, robot dragon that’s tearing up the lobby.
While not as loud as other examples, Naruto the Zoroark from A New World, A New Way sidestory Swarm has one when he wakes up in the palace of the Changling Empire, whom at the time he thinks are Bug Pokemon.
In Game Of Touhou, Yuyuko has this reaction when Nue and her Faceless Men are about to kill her. Yukari is a subversion, she realizes that her teleporting magic isn't working anymore and see that she'll be covered in spiders and die but accepts it.
Tanaka has one after realizing that the list of viable suspects has been reduced to him and Sonia. It's subtly implied that it's not out of fear of getting caught, but because he knows that he didn't do it, meaning only Sonia could be the culprit, something he does not want to be true.
Togami has one that he tries to keep subdued in Chapter 3 when Nanami suggests that she knows he isn't the real Togami.
Never Had A Friend Like Me: Norm the Genie gets a new master, a young girl named Amanda. He becomes rather attached to her and tries hiding his past from her. This is his reaction when she summons him right in front of Timmy and his fairies.
Anti-Cosmo and Head Pixie when they realize they've provoked Norm's anger by trying to kill Amanda, and in the process, rendering the contract that would have protected them from Norm's wrath null and void.
Timmy gets one when Jorgen shows up, and Norm's reaction when Jorgen threatens to destroy his lamp (though that one only last a second since it would be against Da Rules).
In Forward's first "episode" there's the scene where Adelei Niska realizes that he's in the same room as an enraged Jayne Cobb (who he's been torturing periodically for the last several chapters), that Jayne managed to cut himself free, all his guards are dead, and Jayne wants fingers.
In Sisterly Bonds, during the revised prologue, Chouno Ami, has this reaction when she learns that some of the other participants in a tankery exercise stole a Type 90 and brought it to the match. It's also a moment for Ono Yushari, who despite not being in the Type 90, ends up panicking and saying things that inadvertently, and incorrectly incriminate her as an accomplice.
Yushari: "Chono-San, You always taught us to be innovative! We thought-"
Ami: "You KNOW the rules! I can't raise the Type-90. PLEASE tell me it's SDF crewed?"
Yushari(taken aback): "No. We, uh... we borrowed it."
Ami: "You what? That tank isn't restricted by the conduct of Sensha-Dou! It has no legal ammunition, it fires live rounds! Who are they aiming for?"
Yushari: (gulps) "Yours."
Narrator: Ami-Chan slowly looked up in horror. True to Yushari-San's word, the 120mm smoothbore L/44 gun of the Type-90 was pointed directly at the Type-74. There was no doubt an APFSDS round was already loaded in the gun breech.
Ami: "Tell that Tank not to fir-!" (the tank fires, killing Ami's crew and putting her into a coma)
The reaction of most Oarai students after hearing that Saunders will field 20 tanks against them this time, rather than the 10 they faced in canon.
On a more serious note, after Miho is disowned and realizes that the rent is coming due on her apartment, which is more than she can pay by herself.
In Boys Do Tankary, after Vincent gives Darjeeling a coded message saying that he will fire and not miss, she gasps and declares that she and her teammates must find him or they will be taken out very quickly.
The Warblers are actually pretty calm when Blaine, Wes, and David get kidnapped by said stalker, to the point of helping the official police search. Until Kurt finds out, in which a string of "Oh Crap" text-messages are unleashed.
In Harry Potter and the Methods of Rationality chapter 6 Harry has this memorable quote right after his realization, he even literally thinks "aw crap" : “The Dark Lord is alive. Of course he’s alive. It was an act of utter optimism for me to have even dreamed otherwise. I must have taken leave of my senses, I can’t imagine what I was thinking. Just because someone said that his body was found burned to a crisp, I can’t imagine why I would have thought he was dead. Clearly I have much left to learn about the art of proper pessimism.”
In the Heroes universe forum Eclipse, three words have all but become synonymous with this reaction: "Heaven Have Mercy". Having captured Ryan Alcroft and Adele Couteau - arguably the most ruthless and psychotic Battle Couple Eclipse has - a Company agent employs the services of a mercenary illusionist to try separating the two by having them simultaneously witness the murder of their counterparts. Suffice to say, it doesn't end well.
In Lilly Epilogue Family Matters, Hisao has this reaction after hearing that Lilly's family is coming to visit. To put things into perspective, in Lilly's good ending she refused to come to Scotland to live with her parents so that she could stay with Hisao, and Hisao thus fears they will not take her decision well, potentially forcing her to come home.
Used in Seduction when Sarakshi Ishin (who's agreed to let Magnificent Bastard Tora Igarashi take off her shirt if she loses to him), realizes Tora knows the person he just defeated isn't a guy, but her dressed as one.
Discord: You know, for a second there, even I was sure it was going to work.
In Atlas Strongest Tournament, both Blueblood and Fido have this reaction when they find themselves facing Rarity in the preliminaries. The prince recovers quickly, but Fido panics, throws the match, and runs away... right into a wall.
A Brief History of Equestria: According to Clover the Clever's recounting, the Windigo present in the cave had this look on its face when Hurricane let go of his hate (triggering the Warming and the Windigos' extinction); she found it satisfying.
The twisted Dark Fic "Pattycakes" has a literal example. After spending the entire fic as a prisoner, with a badly derailed Fluttershy attempting to Mind Rape her into an infantile state, Rainbow Dash messes her diaper and is so terrified by the situation that her will breaks and she starts believing herself to be Fluttershy's baby (this was later retconned into being the effects of a mental regression drug Fluttershy created, since it generally takes more than an afternoon to totally shatter someone's will). Scootaloo gets a similar reaction to the same stimulus in one of the endings, after drinking something doped with an irreversible dose of the aforementioned drug.
In The Bigger Score, the PHL team raiding a fortified conversion bureau discover the Queen making a personal visit to the place, leading to a Mass "Oh, Crap!". It gets even worse when they discover the Tyrant is going to visit Boston, which is a stronghold for most of their activities.
Narrator: But when she got to her older sister, that's when her heart started racing with fear. Remember when I said that Teru seems to lose control when she gets angry? Well, this is happening now. And with a metal pipe and a box cutter in her possession, this is not going to end well.
The Slender Man ficBy the Fire's Light, features a massive one at the end of the fourth story in the six story cycle when Jared Holloway realizes Detective Carl Rourke has accidentally created an ideal situation for the Slender Man to off both of them.
In the Original Series fic Insontis, one of the security guards literally says this when he sees Spock notice someone messing with the de-aged Kirk. He promptly dispatches some others to deter Spock, "before we have some dead humans on our hands."
In the fanfic Written in the Stars, this is the reaction of Fem!Kirk Prime when John Harrison reveals himself as Khan.
Harrison: My name...is... Khan. Kirk: (sensing her counterpart's dread) Who is he? Kirk Prime: ...Oh...shit...
Shortly thereafter, a double one from Crewman Yasmin Sherazi and Chief Sally Blackhawk upon observing the above.
Sherazi:Kiopek oghlu. That's a Klingon Bird-of-Prey. Blackhawk:(into radio) Starfleet Command, this is COS. Sally Blackhawk of Listening Post Two-Zero-Four-Romeo-Tango, authorization Charlie-Papa-Oscar-3255-Alpha-Whiskey-24827! Case Zulu! Repeat, Zulu, Zulu, Zulu! Details to follow!
Plenty of these abound within Streets Of Rage Saga, but the crowning one (as of this writing) has to be during the epilogue of the fourth story in the series, The New Syndicate: The Syndicate has kidnapped and attempted to mind-wipe Blaze. It seems to have worked at first since she can't recall her name or any of her past memories when asked...but they weren't counting on hearing anything contrary mere minutes later. So cue the man in charge turning pale when he hears this line:
Through A Diamond Sky has a couple. A minor one is when the leader of the Iso colony is being rude and realizes that the visitor asking questions isn't Clu, but Flynn himself. The second, larger, one is when a Mook realizes that they just made the fatal error of trying to kill Tron.
The reaction of the entire "Wargods" strike force and the player when the GTD Imperieuse jumps in just as the Wargods were on the cusp of victory against the GTD Carthage, fully-armed and fresh, and outgunning all of the remaining Wargods ships combined. Things go downhill from there.