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 ''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.”
Used in Seduction when Sarakshi Ishin (who's agreed to let Magnificent BastardTora 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.
In the Star Trek/Babylon 5 fan-made spoof film Star Wreck: In the Pirkinning, this happens more often than would be reasonable to recount here.
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.
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.
Freeman's Mind, where Gordon Freeman finds out the hard way that the soldiers pursuing him in Black Mesa are learning from their mistakes...
"Okay...natural selection; the dumb ones are all dead, so the survivors are a little bit smarter!"
Used as a Precision F-Strike in Kira Is Justice, when Justin realizes L Near figures out Kira is in Chicago. He literally thinks, "Oh, crap."
Part 2 starts out with the Rangers who think they outsmarted the Zordonians after moving, realize they've been found by the Zordonians—by watching their attack on the news.
Later, a hydra eats Nightmare Moon. And she escapes by turning into smoke and forcing herself out their mouths. The hydra then realizes that she is very, very ticked, and a Curb-Stomp Battleensues.
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.
The cop in New Zork freaks out when Paul breaks the handcuffs that were supposed to have neutralized his Super Strength.
The Hunter stands in stunned amazement when John lifts the river.
Grunnel has one when he realizes that Paul isn't mind-controlled after all.
There is a collective one amongst the Raleka and skahs wizards when Sapsa hits Paul with an enormous burst of flame, and Paul says, “That was lovely! Do it again!”
When Shag and Varx reveal to Jeft that they'd told the real Dalns gods what was going on. “Did you want gods pissed at you, Jeft?”
And speaking of, it's almost a given for everyone to react in this way any time any Eldritch Abomination, such as Dynacide, shows up.
Mr. Incredible: My God... WHAT HAVE THEY DONE?!
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.
The twisted My Little Pony Friendship Is Magic fanfic "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.
Happens in chapter 8 of Ace Combat: The Equestrian War. When The Burning Talon's laser destroys the gates of Cloudsdale, Lightning Bolt, Derpy and Soarin' just stare at it, realizing they are screwed.
Ironic Echo: the griffins have the same reactions two chapters later when said superweapon is destroyed.
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.
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:
In the Katawa Shoujo fic 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.
