This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Stargate SG-1
Anubis, both before and after "Lost City".
The Goa'uld themselves. These foot-long snake-worm-things with fins will take complete control of your body and use it to live like a monster for thousands of years. They have access to all the original person's memories, so if they want, they can impersonate that victim almost seamlessly.
Take your pick of how they enter the body. The Goa'uld prefer the back of the neck, while the Tok'ra prefer through the mouth. In the case of Tanith, he entered Hebron's body through his throat!
The Goa'uld enter through the back of the neck (usually) because they don't want to remember the look of horror on the host's face every time they look in the mirror. The Tok'ra enter through the mouth...because in their case the host is willing, so no look of horror. And they also find the scar on the neck the Goa'uld entry method leaves unsettling.
The Replicator-ized Merrick from The Ark of Truth certainly qualifies.
The Replicators in general qualify. Nigh indestructible techno-bugs that devour anything in their path and get smarter the more there are of them? Not to mention the Mind Rape the human-form Replicators seem to enjoy so much. Yikes.
The Ori and possessed Doci. If the concept of being burned alive for not worshiping isn't nightmarish enough, that fire skull form is.
Season 9 Episode 17... "Scourge." Prior bugs that bite you, lay their eggs in you and then eat you from inside out. If you're lucky they'll just consume your entire body in seconds.
"A Matter of Time", when Carter explains what will happen to Henry Boyd's team due to the Black Hole.
O'Neill being tortured to death by Ba'al. Then resurrected. By a machine that he already knows will inevitably drive him insane if he is exposed to it long enough. And Ba'al plans to keep doing it until he breaks O'Neill. At least you can escape a normal torturer by dying...
How about being BURNED ALIVE by die hard Ori followers because you happen to be in a locals body? Obviously not a good way to go if you happen to be a normal person.... but the process in effect does kill two people. The First is obvious, but you're the second as your mind is linked, and therefor, you die as well.
Marduk's punishment in Season 5 episode The Tomb. This guy was locked in a Sarcophagus and eaten alive by a carnivorous creature while the device (already revealed to drive frequent users insane) healed him, over and over again. To make things worse, he actually left his host to take over the creature, meaning his original host regained control of his own body just to be eaten alive by Marduk to the point where the Sarcophagus couldn't heal him anymore.
The infestation flies in Bane. You get stung and your DNA changes you from the inside out such that ten large dragonfly-like insects burst out of your body, but not before you undergo disturbing physical transformations.
The fate of the poor Egyptian scribe that was chosen to be Apophis host, being forced to watch as Apophis comitted countless atrocities across the galaxy for thousands of years, with no control of his body. When he finally regains momentary control while Apophis is sick and dying, the man begs miserably in ancient Egyptian, with Daniel being able to translate, that he's been aware and helpless all this time, and he wishes for nothing but death and to be buried by egyptian custom. He doesnt even get that, Anubus eventually forces SG-1 to return Apophis to him so he can keep him alive and torture him. Its not until Apophis final death that the unnamed scribe finally knows peaceful oblivion.
The Ancients and their status as Abusive Precursors. They arent ACTIVELY malevolent, but have left enormous messes behind during their time in the physical universe, especially the Replicators and the Ori, and refuses to help against them because of their sudden decision to cling to a Prime Directive. Thanks, would have been nice if you had stuck to that thousands of years ago.
The Asgard can come off as this before they've been proprerly established, since they are the spitting image of The Grey. Once their character is more established, some people see them as Ugly Cute.