Star Trek II: The Wrath of Khan gets away with a lot because the PG-13 rating didn't exist back then, so the movie went as far into PG as it could without getting an R rating.
The thought that whatever happened on Ceti Alpha V since Kirk marooned the Botany Bay survivors there was sufficient enough to drive Khan of all people to the point of utter madness is pretty nightmare-inducing. In Space Seed, Khan was himself a case of Nightmare Fuel; in the movie, he's gone completely psychotic.
A Puppeteer Parasite is deposited into a helmet, which is then placed onto a restrained crewman's spacesuit. The crewman, and not any Red Shirt, but Pavel Chekov, is helpless to do anything but scream helplessly as the thing crawls into his ear.
We see one of the scientists from Regula One get vaporized by a phaser. It's not quite an Instant Death Bullet, as we can hear the man's quickly fading scream of agony as he is vaporized.
Some of the injuries suffered during the battles between Enterprise and Reliant. Scotty's nephew, who we find horribly burned, and another crewman in the torpedo bay who gets engulfed in flames during the final fight.
Khan's "pets", the Ceti eels. Two to three-inch long worm-like creatures with pincers that burrow into a person's ear and attacking their brain, making them easily controlled and very susceptible to suggestion. Even worse is when the captain of the Reliant fights back against the creatures, and kills himself with a phaser set to disintegrate. That scene alone is why this troper hasn't watched that movie all the way through in years. Yuck.
Forget that's it's science fiction, the scene where Khan first puts the things in Chekov and Terrell qualifies Star Trek II as one of the best horror movies of all time. The way Khan's looking at them dispassionately as this happens makes it worse.
Similar creatures make an appearance in the 2009 Star Trek film, used by Nero on Captain Pike. What could be worse than a bug being forced into your ear? A bug being forced into your mouth.
Captain Terrell, turning his own phaser on himself and firing. Its the way the actor plays it. He totally sells it. Truly horrifying.
Though we don't see them for very long, the adult forms of the Ceti eels. Khan quite literally plucked two of the young ones off it's body, the thing had quite a grip, and frequently made a very unsettling sound.
There's actually a number of things in this movie that are unsettling: the hanging corpses in the space station, Khan's finale where his face is half burned...
The Novelization makes it even worse: we get backstories for the hanging corpses, and learn how they were all tortured to death. Graphically.
I've done far worse than kill you... I've hurt you. And I wish to go on... hurting you. I shall leave you as you left me, as you left her... marooned for all eternity in the center of a dead planet... buried alive... buried alive...
The worst part of that is, in a way, Khan made good on his threat. Spock is forced to save the Enterprise at the cost of his own life, and while Spock was able to come back form the dead, it was at the cost of the original Enterprise.
The crew of Regula One murdered and hung like sides of beef in a freezer. The novelization goes into detail about Khan's stop at Regula, which is even more nightmare-inducing.
Pay attention to the sound effect that plays when someone is vaporized with a phaser. It's not just the energize sound of the phasers. There is also the echoing sound of a scream.
Peter Preston's mangled body.
What we are verbally teased to what happened to Khan and the crew of the Botany Bay during the fifteen-year gap between Space Seed and this movie. Ceti Alpha Six, a planet close to the Edenlike Ceti Alpha Five, exploded, shifting the course of Ceti Alpha Five just to the point where the environment becomes a hostile, barren wasteland and the only indigenous life form are the aforementioned Ceti Eels, which managed to KILL MORE THAN TWENTY MEMBERS OF HIS CREW, INCLUDING HIS WIFE WITHIN A FEW MINUTES, causing him to go down a brutal Sanity Slippage!
It's not even made clear that Marla McGivers suffered that fate after the disaster. It's entirely possible that it happened soon after they landed.
For that matter, how the movie sets up Khan's big reveal to Chekov and Terrell on Ceti Alpha V. The two beam down to a barren, dusty wasteland and hurry into what they think is an abandoned storage locker. In snooping around, Chekov discovers the words "SS Botany Bay" etched into a belt, which he immediately connects to Khan and goes into a Stage 4 Freakout, telling Terrell to leave immediately. But when they open up the door to go outside, you see Khan and the rest of the Botany Bay survivors just standing together on a hillside waiting for them, all decked out in creepy nomadic clothing. Very well executed nightmare fuel indeed.