- The Star Trek series of novels 'Invasion!' The invading force are basically hell-demons from old Earth mythology that want to take Earth for themselves because they believe they are entitled to it due to living there before humans even existed.
- In First Strike they try to kill McCoy by burning him in a wicker man and their method of attack in 'Soldiers of Fear' is a beam of literal Nightmare Fuel. It's a weapon that projects feeling of terror and images of each person's individual worst nightmares so strong that it can completely destroy a person's mind if exposed to it for too long. And Deanna is empathic, which means she felt/saw the nightmares of every member of the crew of over 1,000. Not to mention the imagery described on Brundage Station and Data's completely detached, emotionless reaction to it while the rest of the trained Starfleet officers were freaking out.
- Also, poor, poor, poor Julian in Time's Enemy. Imagine having all your friends die and your ship almost completely destroyed in battle. You try to send out a distress call, only to discover that you have been thrown so far back in time that humanity is still in amoeba form, so there is no one to rescue you. You could just put yourself out of your misery...but wait. Someone has to take care of the Dax symbiont, the only other survivor of the crash, who is a slug like creature who can't talk without a host body. So you spend decades slowly going mad with nothing to do but write medical notes and no one to talk to but a slug who can't even hear you. Then, imagine you are the Dax symbiont. You can't see, hear or communicate, can only move around within your 1m square tank. And you have to live there, slowly going mad for 5,000 years. At least Julian got to die after about 80. Then imagine finding out that this is going to happen to you and you have almost no chance of preventing it.
- The scene where members of a Bajoran rebel cell die in agony from having only half of their molecules rematerialize after trying to transport over too long a distance.
- And then there's the acid burns Julian and Kira get from that shape-shifting alien. Especially the stubborn way they continue trying to go on without medical treatment, including Julian climbing down several decks with hands that were blistered to the bone.
- The scene where Julian is trying to find said homicidal shapeshifting alien in the pitch black infirmary, and the scene when Julian and Kira are fleeing from a whole swarm of them that have assumed the form of giant, robotic insects that make shrill clicking noises and get trapped in a turbolift shaft. Also, the shape-shifters can't see you, but they can certainly hear you.
- The Star Trek: Voyager novel "Echoes" has a planetary mass made entirely of dead bodies, more than 300 billion corpses, with 3.5 billion more arriving every 2.5 hours. By the time the action starts this has happened 90 times already.
- In the first issue of DC's Star Trek Volume 2, the Salla of the Nasgul was able to kill a renegade seeking asylum aboard Enterprise merely by pronouncing a death sentence across a comm channel.
- The Doomsday Machine mentioned for The Original Series? Another one shows up in the novel Vendetta. It's bigger, it's faster, it's angry, it's haunted by yandere ghosts!
- TNG never got a Mirror Universe episode, but the book Dark Mirror gives it a go, and it's nasty. Troi as Mind Rapist and Picard as a murderous psychopath were bad enough, but then Good!Picard discovers that this universe perverted William Shakespeare into a twisted parody of the literature we know (specifically, the "pound of flesh" scene from The Merchant of Venice.) He can't even bring himself to look at his antique copy of The Bible (presumably he wants to sleep sometime).
- The Deep Space Nine novel The Siege. Three words: Changeling Serial Killer. And he's creative. The carnage that ensues wouldn't be out of place in Se7en.
Nightmare Fuel / Star Trek Expanded Universe