And then there's Species 8472, for the Body Horror they can inflict simply by touching you. They scare the Borg as much as Locutus and the Borg Queen scared some of us.
It's not what they can do to you — it's that they can defeat the Borg. And not just defeat the Borg but do it easily. To put this into perspective, whenever a Borg cube appears in Federation space there's usually a dozen or more ships mobilized to fight it and even then there's heavy casualties. At one point an 8472 ship was drifting, unharmed, among a bunch of Borg cubes, lazily taking pot shots at them and blowing each one away with one or two hits.
Just remember their introduction. Two Borg cubes float towards the camera and the 'We are the Borg...' speech is heard. BEFORE THEY FINISH, 8472 weapons fire and both cubes go BOOM without a chance to fire a single shot. It's that infamous speech trailing off as the cubes turn into nothing but debris that catapults it into High Octane.
Species 8472 were introduced in an episode featuring a small mountain of mutilated Borg corpses. Gah.
And later on, they blow up a Borg planet. If the Alderaan scene is scary, imagine this being done by a couple of Voyager-sized ships, with the beams first converging on a central one before hitting a planet - and instead of clear "Hit and Boom" one sees as the planet disintegrates piece by piece!
The creatures the Equinox crew harvested for their advanced warp drive were creepy, and they popped out of portals and as such could attack from anywhere without warning. Complete with monster's-eye view of screaming crewmen as the creatures pounce on their faces. And what they do to you if they get you is at least as bad as Species 8472.
It doesn't get worse than the Vidiians, though. Afflicted with a disease that wastes their bodies to the point where most of them make your average zombie look like a GQ model by comparison, they attack ships to harvest crews' organs. Instead of the usual ray guns, their weapons teleport organs right out of victims' bodies. Skin is in demand as well, and many a Redshirt has been taken away only for a Vidiian to return still looking pretty rotted... except for the face, which now has human skin that doesn't fit very well. And only the face, not the rest of the head, furthering the glued-on-skin look.
"The Thaw" in which members of the crew are trapped in a dream-like computer program where they are held captive by, ridiculed and almost killed by, not a Monster Clown but a whole bloody ''monster circus''. The clown was the ringleader, played by Micheal McKean as a Large Ham. The part that I remember the most is when the whole circus sings out "A VI-RUS! A VI-RUS! HE THINKS WE ARE A VI-RUS!" in a chillingly demented way.
"Scientific Method" in which the crew are being experimented upon by invisible (phased) aliens. When Seven of Nine alters her optical whatevers, we see the crew walking around with 'things' sticking out of them while being followed by alien scientists like labrats.
And for extra pants-soiling fun, the scene where one of the aliens walks up to Seven and starts adjusting one of the unholy devices attached to her face. And we never get to see what it looks like. And Seven absolutely cannot react to whatever horrors she sees or else she would give the game away to the aliens and they would exterminate Voyager's crew as "failed test subjects".
After enough "special moments" like this, the network all but started advertising it as a horror show. "Such-and-such happens on The Sentinel, and then Star Trek: Voyager unleashes another hour of terror." They're right!
Kes screaming in "Persistence of Vision" and "Cold Fire." Major spoilers for the former - one of the best episodes ever - follow.
"Persistence of Vision" gets special points for some of the hallucinations - the Body Horror ones were awful, but perhaps even more so were the more Lotus-Eater Machine ones. Just think... a loved one appears to you and if you listen to and engage the figment at all, even to tell them you know they aren't real, you wind up trapped, staring into space with God-only-knows what going on inside your head (the episode had some Less Is More going; we don't know what happens to you when you succumb and become basically catatonic and that made it worse somehow.) And then the way it ended...
"Cold Fire" also deserves a special mention for that nice scene in which Kes inadvertently causes Tuvok's blood to boil in a nice display of her ever-growing psychic powers.
Those hallucinations and creepy whispers in "One", and the pure terror in Seven's voice when the Doctor goes permanently offline.
Dejaren in "Revulsion". He's basically Norman Bates as a hologram with a pronounced case of Fantastic Racism for organic lifeforms.
Annorax in "Year of Hell" is basically what happens when you give Hitler a Time Machine.
The Xindi Insectoids are enormous computer-animated ants. Industrial Light and Magic gives us all the detail on them you'll ever want and then some.
There was also the automated repair station that turned out to kidnap crew members and fake their deaths so it could use their brains in its computers. Archer blows it up in the end... but the final scene is it beginning to put itself back together.
Worst of all, though, is the much more graphic portrayal of what happens to victims of Explosive Instrumentation. When the ship gets attacked, other Treks have the Star Trek Shake and the occasional sooty He's Dead, Jim person. Enterprise has things like people on fire and screaming, or crewmen blown out into space when the hull is breached, twitching for a bit, and then stopping.
Most of the episode "Strange New World" was creepy, but the worst was when they beamed up the crewman during a storm and he materialized with sticks and debris embedded in his face and body.
Singularity seems like a "Naked Time"-ish episode, where everyone is obsessed with tiny tasks and becomes extremely agitated. T'Pol is unaffected, so she goes to check if Doctor Phlox is also all right. He isn't. He has become so obsessed with Mayweather's headache that he's going to vivisect his brain, seeming identical to the Mirror Universe Phlox, and threatens to kill T'Pol for getting in the way of his experiments.
In Doctor's Orders Phlox experiences hallucinations whilst he and T'Pol are the only member of the crew awake for a trip through radiation that is dangerous to humans. At the end, it's revealed that Phlox was hallucinating T'Pol as well. She was really sleeping along with the rest of the crew.
The above two examples, his decision to support genocide in "Dear Doctor" and his Mirror Universe counterpart being one of the least radically different in terms of personality, has lead more than one viewer to suggest that Phlox is actually a dangerous nut, seconds away from cracking and going on a killing spree!
In a Mirror, Darkly takes the agony booth and shows what prolonged exposure can do to a person. Mirror Archer is apparently insane after ten hours in Phlox's invention; it's just that the culture's so toxic nobody can tell, and even if anyone can tell, they dare not say so aloud; with Forrest dead, he's now captain.
"The Exile." Think serial-killer drama combined with "Beauty and the Beast." First, Tarquin tries to entice Hoshi with a form he thinks will be attractive to her... while whispering in her skull, making her hallucinate him on all the viewscreens in the lab, and generally causing her to think that she's losing her mind. (Again.) When he does make contact, he makes her stay in his house in exchange for his help and demonstrates that he's been rifling through her memories to the smallest detail—never once asking her permission to do this, even her more painful memories—and tries using them to convince her to stay. When that fails and she finds the graves of his previous "companions," he creates an illusion of Archer essentially ordering her to stay and then attacks Enterprise itself. She has to threaten to break his telepathy amplifier to make him let her go. Freudian Excuse or not, that is some major league creepiness.
After the Klingon moon explodes in a massive Planar Shockwave, the USS Excelsior is close enough to not only have to ride out the shockwave, but when they scan the moon, they learn that most of it is now simply not there anymore. They then receive one of the more disturbuing Distress Calls in the history of the franchise, a Klingon, surrounded by flames, screaming in panicked Klingon before the signal abruptly cuts off, followed by a Klingon officer tersely messaging them to tell them that there has been an accident, and that Starfleet's assistance is not required.
The attack on Gorkon's ship, from the Klingons' point of view. The Enterprise, sent to escort them into Federation space for peace talks, unexpectedly opens fire on them, crippling them and knocking out the Artificial Gravity. Two space-suited assassins beam aboard and begin slowly and methodically marching through the ship, shooting helpless crewmembers as they float in freefall, unable to fight back or seek safety. Once they find their target, they shoot him in the heart, before calmly marching back the way they came and beaming back to their ship. Did we mention that, due to the lack of gravity, the Klingons' blood is left to float in blobs drifting through the air, trailing behind the wounded or dead crewmembers, in a rare exception to the Bloodless Carnage usually seen on Star Trek?
Also, the same attack, from the Enterprise crew's point of view. The ship they are escorting is being attacked, and by all indications, it was the Enterprise that did it, with the bridge crew and Mr. Scott urgently shouting at each other unable to agree on what their own conflicting comptuers are telling them, trying to figure out just what the hell is going on before the Klingon ship finally regains control and prepares to open fire on them in evident self defense.
When the Klingon battlecruiser recovers and comes nose-to-nose with the unshielded Enterprise, the ship locks photon torpedos and prepares to fire. Kirk just stares, slack-jawed at the view screen for a full ten seconds. This is the first time in the history of Star Trek that we've seen Kirk falter in the command chair. He doesn't order shields up, he doesn't order evasive maneuvers, and he doesn't charge weapons, or anything else we expect him to do. He just sits there, staring. . .and then he surrenders. It's terrifying.
What sells that part is the rest of his crew's reaction, especially Valeris', you know, an emotionless Vulcan.
Chekov: "Shields Captain?"
Chekov: "Shields UP, Captain?"
(beat) (Klingon Cruiser is now at point-blank range filling the viewscreen, torpedoes armed)
A bit of a fridge example: Since the 1960s, the phaser has represented a sort of holy grail in less-than-lethal weapon engineering; with their ability to subdue an individual or a crowd instantly with no noticeable lasting health effects. This film, however, makes a plot point of the fact that even phasers on stun are potentially deadly.
Star Trek: Insurrection. The flesh stretching process of the Son'a. Only somewhat Nightmare Fuel until head baddie Ru'afo betrays Admiral Dougherty, killing him by subjecting him to a flesh stretching machine. Ow.
Picard's family including Jean-Luc idolizing, Cheerful Child René—one of the very few children that Picard likes— dying in a goddamned fire.
After Picard fails to stop Soran the first time and they're sucked into the Nexus, it winds up destroying the planet they're on. And it just so happens to now include everyone inside the crashed saucer section of the Enterprise. Which means every character we've come to know and love for the past seven years—- Riker, Data, Beverly, Troi, Worf—- they're all dead. We even get to see some survivors crawling out of the ship's remains just as the planet explodes for good measure.
Star Trek (2009). This movie is surprisingly tame compared to most Star Trek movies, but there are still a few moments:
The indistinct voices heard inside the Narada at one point.
The Narada is about twenty miles long, hideously overweaponed, and covered in blades and tentacles caused by uncontrollable Borg growths. There is nothing Accidental about the Narada's Nightmare Fuel.
Everything about the Battle of Vulcan: several starships carrying graduating cadets obliterated and a whole planet with six billion Vulcans sucked into a black hole in less than an hour.
When Spock is choking Kirk to death for insulting his mother, there's a moment, just a moment, when there's a hint of a bloodlust smile on his face. It is creepy.
"Blood and Fire" is about Regulan bloodworms. The ones the Klingons were joking about in "The Trouble with Tribbles". Regulan bloodworms are not funny. Or cute. Or harmless and useful, like the ones in Enterprise. Point of fact, they travel in gigantic swarms, and they eat people alive, and we get to see it.