Durge (pictured on this page for a very good reason) is perhaps one of the scariest villains from Legends. A psychopathicBounty Hunter who made his first appearance on one of Naboo's moons, where he and Asajj Ventress massacred the the local Gungans in a test of their new chemical weapon.
In Star Wars: Clone Wars, during the assault in the Muunilinst capital we're treated to the big reveal that Durge is more than some healing limb factored armored cladded goliath... Durge's reveal of tendrils of muscle and speed are frightening and the music accompaning the scene sounds appropriately straight out of a horror movie. His form of attack on Obi-Wan Kenobi is grotesque to say the least. He uses his body and "consumes" him. Fortunately, though Obi-Wan manages to escape from within Durge. Albeit, in a brief squicktastic moment.
Legacy of the Force. The Embrace of Pain is back, along with evil Jacen (now Darth Caedus). Ben's tortured and forced to watch someone close to him die.
Speaking of Ben, there's a really horrid scene that involves Tahiri playing The Vamp to the poor boy. When he refuses her advances, she then tortures his soldier buddy to death in front of him.
Sintas Vel, wife of Boba Fett, is revealed to have been frozen in carbonite for 40 years. 40 YEARS. Han was already a wreck after just ONE year of carbon freeze. Sintas is an absolute incomprehensible mess after being unfrozen.
Luke Skywalker and the Shadows of Mindor. Why are Cronal's stormtroopers' armor black? Hint: That's not paint. It's a brainwashing armor, which Cronal used to throw all his forces in a suicidal run against his enemies. Luke (a commanding officer during the mission) had to Shoot the Dog and kill them all, which breaks him so much that he quits military service.
The Tales from Jabba's Palace anthology has the story, "Of the Day's Annoyances: Bib Fortuna's Tale", in which Jabba's former majordomo has been captured by the B'omarr monks, who plan to perform "enlightenment" surgery on him. See, the B'omarr are a cult of fanatical ascetics who have adopted advanced science to help them in their goal of pursuing enlightenment: they surgically extract peoples' brains and place them in spidery life-support units, in the belief that this severing from all fleshy pleasures will expand one's mind. You remember that creepy giant spider you saw scuttling through the door after C-3PO and R2-D2 entered Jabba's palace in ''Return of the Jedi"? That was a B'omarr "brain spider". Picture Bib, locked in the palace, sitting in the dark, hearing the slow, creaking approach of a surgeon's cart...
In-Universe example in "The Krytos Trap", book three of the original Rogue Squadron novels. At the novel's climax, the Super Star Destroyer Lusyanka emerges from its hiding place inside the planet-encompassing cityscape of Coruscant. As Wedge contemplates how in the world Emperor Palpatine managed to put it in there and have nobody aware of it, he comes to the conclusion that thre's two possibilities. Option 1: Palpatine was so powerful he was capable of using More Than Mind Control on thousands, maybe millions of sentients and wiping all memory of seeing Lusyanka installed. Option 2: Palpatine simply had every last one of those thousands to millions of witnesses Killed to Uphold the Masqueradeand nobody ever noticed. He's honestly not sure which option scares him the most.
The Dark Side ending of the first game from The Force Unleashed. After killing Darth Vader, Starkiller tries unsuccessfully to attack Palpatine. Next thing he knows, Palpatine grips the Rogue Shadow with the Force and, with Juno Eclipse still inside the ship, throws it on top of Starkiller. The last thing Starkiller sees is darkness until he wakes up on an operating table, finding himself being clad in a suit of life support armor. Add some last-second Eye Scream, and you'll wish you'd chosen a different final boss.
The second game's Dark Side ending would also count for some. Starkiller raises his lightsaber, ready to end the threat once and for all. Suddenly, a blood-red lightsaber emerges from Starkiller's chest. The attacker decloaks, revealing a hooded figure. RahmKota charges. The hooded figure whips around, blocks all his attacks, and flings him into his Rebel escort. Then, he sends them flying to the ocean below. Vader stands over Starkiller, and says that he lied when the cloning process hadn't been perfected. The hooded figure reveals himself. His face is a perfect image of Starkiller, only devoid of ANY emotion. That has to give one chills.
How about the downloadable Endor level from the The Force Unleashed 2? It follows the alternate dark side ending of said game with how differently things would have played out in the movies had Vader's evil Starkiller clone been a success. Taking place during Return of the Jedi, Vader sends the clone down to Endor to kill the Rebel forces trying to take out the shield. Throughout the level, evil Starkiller mows down all the rebel soldiers as well the Ewoks and successfully kills Han, Chewbacca, and Leia (it was implied that Luke froze to death on Hoth in this timeline). And of course there's a scene afterwards of the Emperor proudly announcing the Empire's final victory and killing Vader upon realizing his secret betrayal. The whole level is basically one huge case of "right in the childhood."
Even worse is how evil Starkiller kills Chewbacca: by using him as a live shield when Han attempts to open fire at him.
Just be thankful it didn't show what he did with C-3PO and R2-D2...
The Force Unleashed sequel has a level on a Nebulon-B frigate. The ship is boarded by unknown forces, led by Boba Fett, but as you go on through the level, you learn that what your facing is terrifying. The spider droids latch onto you with razor-sharp pincers. The infantry can teleport away from your lightsaber strikes, and have cybernetic upgrades along the lines of Grievous. The giants have scalding hot claws specifically designed to cleave through durasteel. The walker could crush you like a bug, and has a screech that sounds like a demon had it's vocal chords ripped out, and combined with nails on a chalkboard. As you progress through this level, you'll learn that this contingent of Elite Mooks are called the Terror Troops for a very good reason.
There was a webcomic called Evasive Action, which described the lives of three Padawans who survived Order 66 and went into hiding. They were on Felucia when Order 66 was issued, and in a convenient spot to watch Aayla Secura get shot down by her own troops◊. Take a look at the background image of Aayla's Dies Wide Open expression... yeah.
Destiny's Way mentions some of the critters employed in the Yuuzhan Vong Sentient Sacrifice. Flaying knives, flesh-eating beetles... We knew already that it wasn't a barrel of laughs, these being the Yuuzhan Vong and all, but still...
In The Thrawn Trilogy, Joruus C'baoth's Mind Rape of General Covell. Imagine a military officer having to relearn the concept of obedience!
From the same books, Joruus' fascination with controlling people and moulding their entire existence according to his wishes. And the fact that Thrawn wins him over to his side by bribing him with Leia's unborn children.
"He would smile, and speak politely, and then he would take her children away.
The Ghorman Massacre, an event that brought the future Grand Moff Wilhuff Tarkin to the Emperor's notice. In the wake of the declaration of the Galactic Empire, tax protesters on the planet Ghorman staged a peaceful demonstration on a landing pad in order to prevent Tarkin's ship from landing. Tarkin simply had his ship land on top of the protesters. In the Legends mythology, this event was what shocked enough people that the Rebel Alliance was able to firmly establish itself.
The whole entechment thing. Draining the life forces of living beings and prolonging their agony to use the energy to fuel the race's machines.
From the Star Wars Tales short comic, Darth Nihilus strips a Miraluke colony world that's hosting a Jedi Enclave of all life: save one.
It is revealed that the Death Star was built using convict labor over the prison planet of Despayre. This labor force was executed and replaced with enslaved Wookiees once it turned out that they were incompetent. Once that was done, Tarkin transported the entire work crew, along with their supervisors, to Despayre...which he then blew up, killing millions of prisoners and thousands of loyal Imperial personnel, both to test the laser's power and to eliminate loose ends.
In the audio book of "Nightlily", we hear Trevagg get his comeuppance. It's as agonizing as you'd expect.