In "Countdown to Extinction", the evil mad scientist Dr. Arkeville gets electrocuted and is treated for his injuries by being made into a cyborg. The result is this◊ delectable bit of Body Horror.
In "Dark Awakening", Zombie Optimus Prime and his Heroic Sacrifice that involved bits of him being blown apart, he ends up without an eye and an arm before his death. The first act had Optimus Prime terrify young Daniel after the lights go out.
Webworld and the Torkuli in general. They are not above lobotomisation to cure their patients of their insanity and speak in a Creepy Monotone. The fact that Cyclonus (who signed all those forms to have Galvatron committed) couldn't do anything to stop them from them implementing Maximal Intervention (by use of the Ayla, insects that have a symbiotic relationship with the planet) on his leader is just the icing on the cake here, so much so that one could almost root for Galvatron once he decides to fight back.
The Energy Vampires (which other than the name, are pretty much a robotic version of the classic Romero zombie) from "Dweller in the Depths" are really creepy. They lose all their coloration, their eyes glow, and they advance slowly but utterly implacably.
How about the entire episode? The Dweller in the Depths, as the Transformers Wiki notes, plays out like a toned down horror movie, which makes sense given that it is inspired by H. P. Lovecraft. You get to see some lovely injuries. First off, during the flashback, the scientist has one of the Dweller's tentacles destroy one of his faces, and when he asks for permission to destroy it, you get a brief, but lovely shot of an utterly wrecked mess of a face that is covered by a mask.
The Trans Organics after the Decepticons awake them. Thanks to the fact they are half organic and half cybernetic, they are straight out of a monster movie. The Decepticons are pretty quickly overwhelmed, with Cyclonus getting his shoulder slashed, and a Sweep getting a very large chunk of his shoulder bitten off, which when it crashes to the ground, has lines of electricity sparking everywhere.
The titular monster is just as scary. It gives some very terrifying roars, getting grabbed by it will get you drained of your energy to serve as a minion of it, and the netting it can shoot from its mouth is near impossible to break out of before you are drained. Its physical resemblance to a merge of Jabba the Hutt and the Sarlacc makes it especially freaky. Oh, and it can move incredibly quickly despite being a slug.
When Springer goes to try to save Wreck Gar, the Dweller attempts to bite him. Okay, Springer manages to jump over it, but had it bitten him, it is not a very far stretch to presume it would be quite messy. And when he breaks Wreck Gar out of the Dweller's back tank, it appears they are safe. And then a Wham Line where Wreck Gar, says "Feed me!" before turning Springer over to the Dweller.
And when Ultra Magnus and Arcee come across Galvatron, he openly declares that if the Dweller gets him, he will be pleased with the idea that he will kill Ultra Magnus and Arcee before he dies. While Galvatron has been made into a punchline throughout much of the third season, this is one of the rare post Movie instances where he becomes a genuinely scary villain, mostly thanks to the music, the way the scene is animated with him slowly approaching the two Autobots, and Frank Welker's voice performance.
The Hate Plague from "Return of Optimus Prime" spreads across the entire planet, so everyone has to see everyone they love go insane and start attacking them, knowing that just a touch means they will lose their minds as well...
The eponymous disease from "Cosmic Rust". It's leprosy for robots. The Autobots even call up video archive footage of a 'bot collapsing to the ground and crumbling to dust from it. The ominous warning message the Decepticons activate does not help.
Antillan Autobot: If Cybertron be your home, far away never roam. Hear my message, listen and fear. Danger comes, the end is near! Just like us, you soon will rust. All shall be turned to dust.
Rodimus' vision quest into the Matrix in "Five Faces of Darkness, Part 2".
"The Secret of Omega Supreme" shows that, during the original war on Cybertron, Megatron used a machine called the Robo-Smasher to brainwash people into becoming Decepticons unwillingly. Omega Supreme is attacked by the Robo-Smasher but manages to destroy it before he can be changed completely into a Decepticon, but doesn't escape unscathed. He's forever completely unable to feel any emotion but hatred due to being partway turned into a Decepticon and is considered a social outcast among the Autobots due to his dreary outlook on life. He gets slightly better by the episode's end, but that kind of backstory probably hits hard on anyone if they or a loved one suffered from a mental or psychological condition due to trauma or abuse.
The prospect of Unicron's revival in Ghost In The Machine. Any kids who were scared of the Planet Eater in the movie had to be spooked by the sight of his disembodied head with its eyes restored.
On that note, the eyes had to be stolen from Metroplex (and later Trypticon after one of the eyes is broken during a struggle) due to the sheer size required. We're treated to Metroplex bellowing angrily to try and scare off Starscream as he loses his vision, and then transforming and stumbling around blindly in a panic. It's rare for such a giant to be so humanly terrified.
Metroplex: WHERE ARE MY EEEEYES!?
Unicron rotating the stolen eyes in their sockets 180 degrees, so he can glare at Starscream and Scourge inside his own head, can be pretty disturbing.
The Tornadron entity in "Call of the Primitives." Both Autobots and Decepticons are helpless against it. It proceeds to suck the lifeforce out of everything on both Cybertron and Earth. If it hadn't been for Grimlock miraculously avoiding getting drained and stopping it by accident, it would have destroyed the universe and left everything a lifeless husk.
In general, the ease with which these sentient robots can have their moods, personalities, and memories deliberately altered or erased would be played for Existential Horror in a more serious work, but here it's presented with as much gravitas as you'd expect from a cartoon of its era.
Galvatron's plan in "The Rebirth" 3-Parter: First he leads an assault on Autobot City and steals the Key to the Plasma Energy Chamber. Then, he leads an assault on Cybertron itself and despite losing several members of his army, sucessfully beats the Autobots and has the Combaticons (for some reason) steal the Autobots' power packs and use them as fuel for a giant rocket engine. Then, after the other Decepticons rejoin his side, Galvatron pilots Cybertron to above Earth's sun and plans to open the Plasma Energy Chamber into Earth's sun and let that wipe out Earth and Cybertron! It takes a Deus ex Machina to stop this plan and even then, Galvatron and Zarak are planning by the episode's end to build a new planet and try again. Even worse is despite Galvatron's "most genocidal and unbalanced scheme ever" (as the Transformers Wiki puts it), he's completely lucid and calm, only showing his infamous temper when the Decepticon Headmasters and Targetmasters returned and he would have blown the -Master partners to pieces had Zarak not revealed he had the Key to the Plasma Energy Chamber.
◊ delectable bit of Body Horror.
