This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Cyborg 009
In "Little Visitors", we get to see the result of the alien slavers attacking Shanghai... repeatedly. After destroying the city, they rewind time just so they can experience the 'fun' of slaughtering everyone again.
"Frozen Time". Joe gets stuck in his Super Speed mode. He can see everyone, but can't interact — simply touching them while constantly acclerating could be catastrophic. The effects this hason his psyche are swift and brutal.
"Black Ghost Lives!" offers a look into the sort of experiments the organization ran on the cyborgs when they were first converting them. It's just as fun as it sounds.
There's also the part where 004's enhancements begin to screw up, causing him to lie on the ground screaming, while 003 and 002 have no idea how to help him. They're both re-frozen in the next scene, because the scientists have no clue how to fix it either.
There's one especially frightening part where Gilmore - the Team Dad, the one who we see treating the cyborgs as his own children - performing surgery on a just-kidnapped and drugged Francoise (the same woman who he'd affectionately consider his "ballerina" and have help him out, and generally was fatherly towards), while narrating that he was so interested in trying out his new surgery ideas that nothing would have kept him from what he ended up doing.
What happens to Pyunma in "Old Friends" ( a terrible beatdown from a Brainwashed and Crazy friend and later a heartbreaking Shoot the Dog moment, and the fallout during "Nightmare of Van Bogoot" where his body is almost torn apart.
How Nichol/as died in the Psychic Assassins's arc. Having your neck and maybe all of your limbs snapped via telekinesis is a TERRIBLE way to die, and for worse the Cyborgs try to help but even with all their powers, they can't do anything.
In the 1979 arc, Jet has an arm ripped off him. If it was bad enough to see him getting a leg almost destroyed in the 2001 series twice, then this is said scene taken Up to Eleven. Specially when there's a close-up to the poor guy's horrified, pain-stricken face...
And when you watch the scene in its entirety it gets way, way worse: that statue is a giant robot commanded by the bad guy, whose objective is putting his hands on someone the cyborgs are protecting. He takes 002 hostage and proposes to exchange him with the person the group is hiding, but Jet tells them not to give in to the blackmail. So, to show he's not joking, the bad guy rips off his arm, only for Jet to say once again to his friends not to do it, at which point the statue tightens its grip until he passes out from the pain.
See that allusion to Pyunma's Near-Death Experience in the 2001 series? It's much, MUCH worse in the original manga. As in "mangled to the point all that's left is his HEAD" worse.
Albert's battle with his robot double in the manga's "The Bizarre Machine" (the story adapted into "Man or Machine?") is a little more bittersweet than the ultimately heartwarming anime version, mainly because viewers are treated to a brutal few panels of the fake Albert stamping on a nest of owlets to silence their peeping (in an attempt to hide from the real deal), followed by him murdering the mother owl.
In "The Snow Carnival", the Snow Witch murdering tourists by chopping their heads off, followed by the revelation that the Snow Witch is Linda, a young woman who's being gradually converted into a cyborg due to her organs being harvested for her adoptive sister Lena.
Conclusion: God's War (Manga and Novel versions)
The sight of lynched corpses in G-Junior's chapter, as part of the mysterious incidents occurring in the Amazon.
The mysterious deaths occurring in the UK involve several people having fallen to their deaths, with the tops of their torsos being grotesquely twisted around so that their chests and faces are facing backwards. This is shown in QUITE a few panels, with several corpses displaying this mutilation and all bearing horrified expressions.
Joe experiencing Mind Rape from Hisui as Queen Himiko, who's induced him into having a creepy hallucination of having sex with her. It leaves Joe traumatized to the point where we see him in despair, unshaven and with an emaciated face.
Joe's university peer Shiori experiencing a particularly gross and messy death involving her eyes being gouged out and her head exploding, courtesy of Hisui, who's since become "Queen Himiko".
When demonic creatures descend on Tokyo, there's one example overlapping with Narm that sets up what will befall the entire team: Jet is suddenly snagged by a demonic alligator, though oblivious at first. As Pyunma can only watch in horror, Jet is bashed up against walls by the alligator, then spun around in its mouth until it CHOMPS down- sending his upper half shooting up into the sky and spinning out of control. Pyunma has to then carry Jet's upper half off to safety, risking swimming through the alligator-infested waters.
The other cyborgs being laid waste to by demonic creatures and horribly mutilated, necessitating new upgrades for each. Among the numerous mutilations: Francoise has both her eyes gouged out and loses her right arm, Albert loses BOTH arms and his right leg, G-Junior's skin is terribly damaged, and Joe loses his left arm.
When the cyborgs start falling to their darkest temptations, Francoise is so horrifyingly broken that she gouges out her newly improved cybernetic eyes, and THEN puts her gun-hand to her head in suicidal despair. She's bailed out of her situation by Ivan, and wakes up in a hospital.
As far as the others go, Jet regresses into a violent street thug and starts taking pleasure in beating up and maiming others, and even pulls a gun on a cop. Meanwhile, Albert shoots out another trucker's tires, and starts to embark on a bloodthirsty rampage. G-Junior starts destroying nature, while Chang burns down buildings, robs safes, and then attempts to hang himself in shame. G.B. attempts to burn down his apartment, while Pyunma and Joe attempt suicide by flinging themselves off cliffs. Ivan has his work cut out for him.
Chang being the first to die via his body messily exploding and scattering his organs everywhere.
After the sacrifices of Pyunma and Albert, the giant Buddha attacks the remaining men on the team, one by one. G.B. loses an arm and is later crushed to death by the Buddha's foot, G-Junior loses a leg, and Jet has his lower half entirely disintegrated.
Jo Onodera's light novel adaptation, which preceded the manga version, has Albert graphically and messily get bisected in battle, which is why he's unable to walk and has to have G.B. carry him off. Jet's maiming by the Buddha was also more dire, with him getting his arms ripped off along with the lower half of his body.