Even within the limits of being a skeleton drawn with stick-figure art, Xykon's expression when he's confronted by the ghost-martyrs of the Sapphire Guard, led by Lord Soon himself in this strip conveys this reaction loud and clear. Later in the same battle, it happens again, after Soon reveals that he knows exactly how to permanently kill a lich. And then Soon has one when he realizes Miko's about to destroy the crystal.
Belkar Bitterleaf, though a hero (arguably), suffers one in #568. After finally getting fed up with an annoying oracle, Belkar kills him. Unfortunately, he also has a Mark of Justice on his head, set to go off when he kills a person within the sphere of influence of a town. And guess what popped up around the oracle's home last week? The name of the town manages to make it even more hilarious.
Elan, Therkla, and Qarr share one in the second-to-last panel of this strip.
Therkla: Did that tree... Qarr: ...just say "Oww"?
Xykon again when his phylactery is about to fall into the Snarl's prison. He has a brief moment of relief when it doesn't, only to get the look again when it instead falls into a sewer with pipes leading to a sewage plant, a labyrinth, and the ocean.
Admit it. You were thinking it about halfway through this page.
And in this one.note For those unfamiliar with the comic, Schlock there is talking to some rogue nanites that have infiltrated his eyes and hijacked them in order to create a simulated space to speak with him. Combat between members of his species half consists of using their extremely potent and adaptable immune systems to counteract the various chemical cocktails their opponents synthesize in an attempt to melt and absorb them. And he's just revealed that the plasma cannon he's been "impotently" waving at the nanites was actually just a familiar visual metaphor for his immune system. They have very good reason to look so worried in that third panel.
Rule 3: An ordnance technician at a dead run outranks everybody.
A twofer in the last row of this comic. Even if it's just a still picture, the last target's eye view of an oncoming missile is never happy.
Rikashar also has a Freak Out after Ariel beats the crap out of him when he tries to abduct her and make her his wife with his reaction following here, and the last panel of the same page is more of an "Aw, shit" after he sees who's caught up with him.
Yet another from the same comic happens in the seventh panel of this chibi-page, which parodies events from that same chapter.
Later, Thaco gets one when Goblinslayer illuminates the darkened sewer, negating Thaco's single advantage, (his ability to see in the dark) resulting in a straight up fight between the two adversaries that Thaco cannot possibly win.
In the same fight, Goblinslayer also gets this, when Thaco remembers he is a Monk and can snatch arrows, making Goblinslayer's ranged attacks useless.
Saves a Fox's entire self-image was that people are not bound by their destiny. When the fated day came when a fox got stuck in her home village's food supply, she snapped its neck in order to spite her fate, and saved the tail as a memento. That's not the Prophecy Twist resulting in her Oh Crap moment... Dies Horribly informs her that the symptoms she described the fox having was that of Sunset fever, something that causes animals to become delirious before dying a horrible, painful, and silent death. Saves A Fox gave it a Mercy Kill before it could suffer the worst effects of it. The look on her face that not only is her entire self-image a lie, but her friend whose name reflecting his destiny is "Dies Horribly" is not able to escape his fate either tells us she's heading right into Heroic BSOD territory.
The Psionic Minmax alt was supremely confident until he realized Kin announcing his intent to kill everyone in the Maze of Many had united all of the survivors against him.
In the webcomic Narbonic, Dave's normal state of being becomes one big Oh Crap moment.
Dan and Mab's Furry Adventures has its share of Oh Crap moments, particularly in the latest arc. One of the better ones has to be Regina's, starting on page 973. Of course, this being DMFA, it's the page's punchline.
Regina:(thinking) Should be easy. I nearly pulped him last time we fought. I mean, it's been what, six years? What could he have learned in that time? * K-shnk! K-shnk!* Dan: I learned to hear thoughts. Among other things. Regina:(thinking) OK. New plan. Piddle self. Run.
Erfworld: Charlie has the distinction of getting one offscreen during this exchange with Parson over the Eyebooks, after just getting Parson to use one of the calculations he owed Charlie to assess whether it was worth giving up the rest of the calculations in exchange for information from Parson.
Charlie: That was clever though, right? Parson: Sure. Determining the decision not to spend all the calculations. Cost: one calculation. Charlie::) Parson: Teaching me that my bracer can make sophisticated predictions about the future? Priceless. Charlie:...:(
Later on, pretty much all of Gobwin Knob (especially Stanley and Wanda, who had been unshakable beforehand) get this when Faq's Turnamancer linked with Charlie manage to force them to end their turn.
Each character gets at least one, but Black Mage, as the resident Chew Toy gets the most of them. It doesn't help him that his face is EASILY the best suited for these expressions.
The universe itself goes Oh Crap when Black Mage becomes the ruler of Hell.
A minor one in El Goonish Shive: Nanase uses her fairy doll to contact Ellen, and tries to wake her up by tickling her nose with her tail. Her reaction when she realises she's about to get messily sneezed on is hilarious.
There's a slightly more major one here. More of an awkward "oh crap" than a dangerous one, but just as expressive...
Valerie: "I told you to stay out of my business, you bitch! Once you're an immortal I will take great lengths to see you suffer in ways impossible for a mortal to understand. Don't think Sam can protect you, he is far too weak!
Zoë (thinking): Wow! Vampire PMS!
Valerie: "We can read thoughts, you know."
Zoë (thinking): Oh crap!
Valerie: "That is an understatement."
"Mecha Easter Bunny" is practically built on a long sequence of these.
Bun-bun when he torches the Mecha Easter Bunny and finds that he's only revealed an unharmed, heavily armed robot.
When Bun-bun pulls a bazooka on the Mecha Easter Bunny and right at its face, it tries to frantically scramble backwards, and its "internal robot view feed" also shows the text ">OH CRAP!!!!"
Mind you, a bazooka shot to the face barely scratches the MEB, leaving Bun-bun to have another "oh crap" moment.
Santa Claus when he realises the MEB, which he built, is about to kill innocent people. "Ho-ho-holy $#!%!"
Santa again when Bun-bun manages to destroy the MEB, and Santa knows he'll be coming after him next. "Ho-oh crap."
Finally, Bun-bun when he thinks he's decapitated Santa and it turns out it's a dummy full of explosives just about to go off.
In "Dangerous Days Ahead": When Hereti-Corp troops led by Mr. Killum disable Riff's robot with an EMP, only to find that inside is actually Oasis, a One Woman Army brainwashed to kill all Hereti-Corp personnel on sight. (Killum: "Oh shi*...")
"Mospinispinosp" is a demon consisting of a snakey humanoid female body (Mosp) with two small talkative snakes (Isp and Osp) for "hair". At one point, Isp and Osp wait for Mosp to apparently be asleep and confide to another demon that she's been helping mortals and betraying the demons. They certainly have an "oh crap" moment when they realise the "demon" was just a sock puppet on Mosp's tail, and when they see the diagram of what she's going to do to them now (which is to make "earrings" to clip their mouths shut).
Later Isp and Osp again when they think Mosp has killed their Demon Lord — and even more so when they find out she failed. "Holy demon-crap!"
"A Time for Healing": Jane, an intelligent zombie who's giving Gwynn a "The Reason You Suck" Speech while preparing to eat her brain and mocking her claims of a Tome of Eldritch Lore that gives her magical powers — when she pushes her Berserk Button and finds out that that's what activates said powers, and they're way out of her league. Her face is not shown at the Oh Crap moment; it's instead indicated effectively by her surgical saw winding down.
"4U City Red - Another Year in the Life of a Villain": An ordinary, non-talking frog (usual line: "CROAK.") is caught in a building after a somewhat literal-minded One Woman Army has been ordered to kill everyone in it.
A Running Gag where Dr. Schlock thinks he's just got out of trouble and then Riff sticks a laser cannon to his head.
In Exterminatus Now, a random paranoid tries to temporarily ingratiate himself in the protagonists so he can hide from "government spooks". The main characters proceed to inform him that those people are likely just foreign businessmen, while revealing enough information to make the guy realize they are government spooks.
And here's the reaction of the original team members when Rogue horribly insults Lothar.
In Two Evil Scientists, a robotic clone of Dr. Wily uses Evil Energy to revive Bass at the insistence of his daughter Cream. It works, and he has a few moments to enjoy his success until he realizes he brought Bass back to life, and he Came Back Wrong.
In Homestuck, Eridan's reaction to his victim Kanaya coming back as a glowing super powerful Rainbow Drinker (the Troll version of a vampire) that just snapped his wand leaving him unarmed while she revs up her chainsaw is priceless.
Even better and even more cathartic? Bec Noir's reaction to seeing PM arrive in the troll's session, wearing the White Queen's ring and looking pissed. Off.
Two from two different characters, one after another. The first is when Rose realizes that it's not a memory when the Draconian Dignitary is in Dave's room with her. The next is when Dave remembers that he's not in his room. He's still asleep on Derse.
Aradia's reaction to seeing Sollux is as cheerful as you'd expect from two friends (or more) meeting up for the first time in real life... right until she realises he's Brainwashed and Crazy.
A three-way version occurs when Jake and Jane stumble into Derse right before it starts falling apart and Dirk comes across them. All three of them proceed to freak out.
Though stoic, the music and editing made it clear that Davesprite got one of these when Jack was prototyped for the fourth time in the middle of their fight.
In Gunnerkrigg Court, Kat and Annie get a pretty good one when faced with a giant crab at the start of third year.