Basically every form of Human Transmutation results in you getting tossed through the Gate of Truth - except for one form: Transmuting other people into a philosopher's stone. You pay no price - it's all on them.
Episode 2 of Brotherhood, "The First Day", is full of this. Ed and Alphonse's bodies disintegrating, the screaming, the blood...
Roy Mustang. Episode 54. What happens when Envy reveals it killed Hughes? Roy's facial expression immediately changes into the Death Glare to end all Death Glares. Not to mention his personality does a complete 180, acting like a demon of unfathomable fury and rage has possessed him to torture and kill Envy in the most brutal, cruel, and frightening ways imaginable.
The ways in which a Homonculus dies in the Brotherhood anime- listening to them scream in terror as we see, in vivid, gory details, 'each layer of the human body being rotted away layer by gruesome layer!
The inside of Greedling. Those huge, demonic faces staring constantly at its victims behind a constantly-shifting, blood-red background.
The armours with souls attached to them that were guarding Laboratory #5. There are sixty-six, or possibly even more revived souls like Barry the Chopper and the Slicer Brothers that cost state alchemists an arm an and leg (or more) to bring back, a vast majority of those souls completely off their rocker, just like the...people... who brought them back.
The thing that Ed and Al created when trying to bring back their mother. All those twisted limbs, the pulsating, the horrible gaping mouth, the eyes and that strained, gasping noise... It's like the creature was struggling to breathe.
Its ribs were sticking out of its chest, and its limbs were halfway through its body in some places. And Al's soul was in its body. No wonder he blocked out that memory.
Shou Tucker himself. The very thought that a man could transmute his wife and later his 5-year-old daughter and her dog into chimeras is just nauseating in all sorts of ways. From Nina's garbled speech, she wasn't even fully aware of what had happened. And then Scar shows up and Mercy Kills her.
The fate of the first Greed. He got melted down to his core....slow and painfully. To make it worse, the Big Baddrank his remains. Greed's reaction to this? Insane laughter.
The making of the Philosopher's Stones...Which involves getting your soul ripped out and trapped in a tiny, rock-sized container... along with probably a dozen more souls. And you are conscious. The whole time. Those screams of despair aren't there for no reason...
Maria Ross's death. She gets flame broiled by Mustang in episode 17, and her burnt corpse is very graphically displayed. It was actually a cadaver created by Mustang, but still...!
Every single time Gluttony stares at the screen.
Envy's true form. As if the idea of turning souls into Phlebotinum wasn't scary enough, this consists of seeing their distorted faces begging you for release from their tortured existence. A melting, dripping, mutating bodymash of emaciated faces begging for their mommies and/or death. The true form is Upped To Eleven in the anime. It's the way that all the faces are moving, all the time...
Envy's Sleep Mode Size. It's particularly abhorrent and uncanny. Looks like the hybrid of a maggot, a human fetus, a caterpillar, and some wide-eyed fish. It also somewhat invokes Vagina Dentata.
The disturbing imagery gets turned up even further in Brotherhood in the scene where Marcoh defeats Envy. Misshapen heads vomiting out misshapen heads and tortured screaming.
Gluttony's true form is shown several episodes/chapters before Envy's. His entire front half splits open, baring his open ribcage, which extends from his jawline to his groin and rakes forward. His entire lower jaw is gone, leaving tusk-like ribs near his jawline, and his exposed, Ouroboros-tattooed tongue slavering in the open air. Looking inside the opening reveals nothing but inky blackness and a single eye, almost exactly like the one in the Door of Truth. And then he goes on an insane rampage, erasing large sections of the landscape with what appears to be some sort of Kamehame Hadoken, but is actually him extending his ribcage faster than the eye can see and swallowing whatever he catches. From the most cheerful, childlike, and seemingly least dangerous and malicious Homonculus, this was a nasty surprise.
And then he eatsEd, Ling, and Envy, and we're treated to an inside view of his stomach; or rather, where everything he eats goes. It is an infinite, featureless plane, with chunks of all the evidence, ruins, and people Gluttony's ever eaten still intact inside. The plane is filled with a similarly infinite ankle-deep sea of blood. Worst of all is how, as Envy fatalistically explains, there is no way out. The place is another dimension: literally infinite. The only thing normal people can do is wander in the sea of blood, waiting to die. Ed finds a way out, but that method isn't pretty either, and if it weren't for Envy's Philosopher's Stone, probably fatal.
The episode...The Ishvalan War of Extermination. Its as horrible and nightmarish as it sounds. We see Armestrian soldiers gunning down civilians en masse, the sheer horror of the genocide, and learn the scary reality of what it means to be a sniper from Riza Hawkeye herself.
Pride what with all the giant mouths and eyes. And the anthropophagy. And the homunculus cannibalism. And all those Slasher Smiles after eating Gluttony. Enfante Terrible indeed. More so in Brotherhood than the manga, since apparently Studio BONES learned a bit when they animated Soul Eater; he grins like Medusa.
Especially in the anime, where he absorbs Kimblee...alive. Worst part is, you watch it from Kimblee's point of view, and those jaws... those horrible jaws... then... CHOMP.
And in the end, when Kimblee reveals that he's still alive within Pride, because the sounds of all the people screaming in agony, non-stop, is like music to his ears.
Here's one in the manga that is more psychological horror than a scary image, but still pretty scary. Riza discovers Pride's identity. Pride is a Living Shadow of eyes and mouths and likes to rip people to shreds or eat them (that's the visually scary part). What makes it even scarier, is that Pride can basically appear anywhere there's a shadow, so for several scenes, Riza is paralyzed with terror just by seeing a shadow near her, as Pride could devour her at any time and could hear everything she said. Luckily, she is able to pass a coded message to Mustang and escape from this, but it's still pretty horrifying.
What happened in Hohenheim's backstory. Waking up to discover that you're the only one still alive in your ENTIRE COUNTRY, have been manipulated into practically causing genocide and thus share responsibility of the horror- and then discovering you've become immortal and the souls of half of the inhabitants of your country are within you, screaming in pain, sorrow and anger every minute? The Scream says it best.
Add to that his realisation that because Homonculus was made from his blood, it mirrored his desires: When he was a slave, he wanted freedom and knowledge, at least subconsciously.
The Cyclops soldiers, which look like the unholy spawn of the Mass-Produced Evas and an especially ugly zombie. The Brotherhood anime has them all awaken with a chorus of horrible screeching. Like millions of souls screaming of unexplainable torture. Equally disturbing is their tendency toward creepy giggling and Psychopathic Manchild behavior which along with some of them calling for their parents strongly implies the ravenous monsters contain children's souls.
When Envy recreated its body using those said Cyclops soldiers. They basically devoured each other and then formed an abomination/blob.
Father's 'true' form in chapter 97, a black thing with huge eyes all over of his 'body', the mouth, and how the black goo-thingy came out of his body.
Chapter 102, when the Homunculi force Roy to open the Gate, and he loses his eyesight even though he didn't do anything.
Mustang: "What are you talking about? Are you with me, Fullmetal?"
Ed: "Huh? What are you talking about..."
Mustang: "It's pitch black... I can't see a thing. Where are we? Can you see any lights?"
The... thing... which was created from Pride using the Gold-Toothed Doctor as 'raw materials' for the transmutation. Sure, he deserved it but still...
The Blind Alchemist Gaiden/OVA. Not just physical horror, either. The sheer psychological shock is pretty disquieting as well.
Chapter 104. Everyone is dead. Everyone. Havoc? Breda? Falman? Fuery? They're dead. The Briggs soldiers in Central and in the East? Dead. Winry? Dead. Pinako? Dead. Gracia and Elysia? Dead. The Ishvalans, the people in Rush Valley, the Youswell coal miners, every cast member that has ever made an appearance in the series is dead, their souls stored inside a monster. Their bodies? Empty.
In Brotherhood, they show the Ishval Massacre. The parts that show the Ishvalan civilians being trapped in the city and mown down mercilessly while they scream for help (particularly images of the children being shot to pieces) is very haunting. The music and Deliberately Monochrome effect do not help.
"What if I was to give birth to humans?" The humans he means? Hohenheim's friends from Xerxes, who are emaciated and barely conscious as they walk with a Zombie Gait. The Emperor is in there, still thinking that he is immortal. And then Father proceeds to nuke them all into oblivion. Those poor souls have been trapped for centuries in an endless torrent of crazed, screaming companions, only to abruptly obtain freedom— giving them just enough time to see the world, and then be blown away to nothing.
In chapter 106 of the manga, Pride's body is slowly falling apart from forcing Roy to open the Gate. So what does he decide to do? He makes a cut on Ed's face and forces his shadow arms inside to take over Ed's body as a new container. You can see the shadows force their way inside and slowly spread across Ed's face and shoulders.
The Brotherhood version, where he gives his speech, then uncovers his eye to reveal that half his face is just a gaping hole into a raging storm of tormented, screaming souls. And then some of his shadows stick out of where his eye socket should be!OWOWOWOWOW. It's heavily implied that Pride feels no pain from that.
In chapter 107, Ed finally regains his right arm. This is a good thing, right? Except... if you look closely, you can see there are now automail parts fused into his flesh where the arm regrew.
Father's original form, "The Dwarf In The Flask",because it seems like he's the embodiment of pure evil, and you don't even expect or even know it, more or less, is somewhat frightening.
Father getting trapped in the gate by Truth. The Brotherhood episode came out, and watching Truth talking with a cold indifference while Father gets pulled in complete with him screaming and sobbing, asking for repentance.
When Lust is burned to death in episode 19. Dear God, that scene. When Roy sets her alight the first two times she gasps in pain, then the third time we get a good look at what's left of her scorched face as she starts to scream. And then he does it again and again and again and she keeps screaming. No doubt she deserves it, but damn.
Then there's Envy's turn to get burnt. The man known as Roy ceased to exist for a few moments, replaced by some wild primitive beast man that happened to look like him. And one of the first things he does is set Envy's eyes on fire!"How does it feel to have the liquid in your eyes boil?!" Though he was talked back to his senses.
The moment in chapter 107 when Greedling punches God!Father in the eye and it shows his hand stuck in his eye socket. Nerves seem to be traveling from said eye-socket, under Greedling's skin, and up his arm, trying to take his philosopher's stone with him.
Episode 41. The scene where Ed gets gored through the stomach by the beam. Edward's bone-chilling screams of pain as the Chimeras pulled it out of his stomach as he simultaneously healed himself. He was burning through his soul to do so. This with him screaming in agony and trying desperately to focus through the pain for just long enough to seal his wound.
The Sacred Star of Milos. There was one hell of a cure for insomnia when the man we thought to be Long Lost Sibling of Julie Crichton, Ashleigh, reveals that he was actually a former bodyguard who murdered her parents, ripped off skin with the tattoo of half the Milos transmutation circle and the face of her brother and grafted both of them to his body. This was just after he impaled her friend and his underling with a sword that opens up to drain their blood so it could fill the city wide 3 dimensional transmutation circle, and before he tore off skin with the tattoo from his body so he could match it up with the one on her body. And we later find out not only was her real brother fully conscious when his face was ripped off, but he survived it when he appeared to give his identity thief a very painful death.
The Gold Tooth Doctor's creepy Slasher Smile, from one of the most depraved characters in the series. Not only did he make the failed Wrath-wouldbes monsters, the bastard slit Riza's throat, nearly killing her.
While he is a bastard for being so willing to sacrifice most of Amestris just to become immortal and being a Dirty Old Man, General Raven really doesn't have any nightmarish qualities about him. However, one of the eyecatches of the episode wherein he's killed by Olivier Mira Armstrong shows Raven with this utterly sinister◊ Slasher Smile, revealing his true nature.
The Liore Riot. Even after Cornello's defeat, Envy ended up impersonating him and used his charisma to turn the populace into a howling lynch mob obsessed with bring "the Father's word" to the world. Disagreements began, and what began as a simple riot became what is described as the single bloodiest conflict in the entire history of the world, full of massacres, destruction and Cold-Blooded Torture. The fact that Liore is still around afterwords is nothing short than a miracle.
This isn't even the first time Envy has pulled this off. The powder keg that was the annexation of Ishval only fully into a war of extermination after Envy took the guise of a soldier who had been against the occupation, offered a seemingly friendly smile to a child to come across like the same guy, then shot that child in cold blood. The fact it can do this kind of thing taking the visage of someone who's either been shamed or who would seem completely OOC doing what it intends to do with their look, yet still get all the desired effects is extremely frightening. Imagine Bernie Madoff using economic fears to fleece throngs of people out of their money yet again from his jail cell, or your staunchly anti-war relative initiating a shootout at the local police department which goes so bad it sets an entire town into lockdown. Envy can do that. In fact Envy gets its kicks that way.
After Scar captures Tim Marcoh, he decides that it'll be easier to travel if Marcoh can't be recognized, so he blows the skin of his face off, complete with lots of blood and a close-up of Marcoh's eye between his fingers that clearly shows exposed muscle. And he'scrying from the pain. All of this happens without the slightest bit of warning beforehand.
When Envy confirms to Mustang that it's the one who killed Hughes - and then shifts into Gracia again, just to rub in the fact that Hughes was killed by someone wearing the form of his beloved wife. It's really quite dreadful to watch the face of the normally kind and gentle Gracia wearing a huge, demented grin as her husband's killer babbles about how great the 'utter shock, the dumb confusion' on Hughes' face was as he died. Naturally, this slams down hard on Mustang's Berserk Button.
Shou Tucker's reappearance as a chimera. ''His spine was fused to whatever animal he was combined with in a way that made his head look upside down. And the fact that Shou talks entirely in a WHISPER after this event.
The scenes in the decaying, bombed out shell of a city. That's WWI era London. While that may not seem so disturbing, bear in mind that in the first anime series, it is said that every time alchemy is performed, someone in that world dies. Even if the manga/Brotherhood 'verse works differently, it's still creepy.
All the freaky shit from the first episode. When Al and Ed were in the Gate and Al was being forcibly pulled in, screaming for his brother to help him while Ed reached for him. Their hands barely touch for an instant and then Ed is screaming in disbelief, anger, and then bloodcurdling pain as he clutches the bloody stump of his leg.
The chimera that Cornello put together to resemble Rose's lover.
The time when Wrath, pre-"awakening", accidentally fused himself with the bed... It's a bit like the Tele-Frag article when you think about it.
When he fuses himself with Sloth and she is literally evaporating because Ed transmuted her into ethanol. The reaction with his body causes his skin to become permanently burned, and he tears free of her while screaming in pain.
Envy killing Ed via a blade through the chest with blood spewing everywhere. Top that off with a close up shot of Edward's pupils dilating as he finally dies. And Envy's freaking huge Slasher Smile as he was doing so.
The Mind Screw moment when you see the flashback of Izumi trying to bring her baby back to life: It looks like the transmutation worked because her baby's body swells and actually starts crying, but it actually failed, and she places her child at the Gate. The creepy shadow arms grab it and yank it back through the Gate while it's still crying. Izumi is shown remorsefully reaching out to her helpless baby as it is pulled away from her. When the Gate closes, she lets out a bloodcurdling scream.
Kimbley's method of dispatching his foes or just people who happen to be in the wrong place at the wrong time.
The death of Basque Grand at the hands of Scar. After Scar deconstructs his gray matter with alchemy, blood shoots out of his ears, nose and eye sockets in slow motion.
What happened to Rose after she was captured during the raid on Lior.
In the video game Curse of the Crimson Elixir, the Elric brothers are sent to investigate the village of Bord'wan with Riza. You find the place in complete shambles—all the houses are blown out and many are covered with bloodstains (even the path you're walking on). It's dark as night, infested with scores of inky-black Golems, and has some suitably creepy music in the background.
An early chapter has the brothers investigating Shou Tucker's house. Know Resident Evil? You'll be getting familiar vibes walking through the mansion, but not through zombies, you'll be looking at the files, and when you look at Tucker's diary, it's clear that he's lost it.
Near the end of the game, Ed's contact with the Crimson Stone causes him to end up in a blank white void. His only guide are blinking red lights, and touching them allows him to see Crowley's memories of his slow and steady descent into complete madness after failing again and again to create the perfect Golem body to place his lover's soul into.
In The Broken Angel (of which Elixir is a prequel to), Carmilla melting into a human-shaped mass of inky-black goo. Her screams of pain and rage don't help matters.
"Can I...eat him??"
The episode where people in a town are infected with a disease that slowly kills a person by turning their skin into a stone-like substance. Made all the worse with the close up of one of its victims: Lydia, an innocent young woman, has her face disfigured so it resembles rotted, stony bark.
The whole thing with being stuck inside the Gate. Wrath described it pretty well. Stuck there. Sentient. No way to escape. And now lets think about Al's body being there, surrounded by all those eyes...
Envy's final form in Conqueror of Shamballa. To put it into simple terms, the movie has Envy as this enormous dragon-like serpent, with razor-sharp fangs, that can move at lightning-quick speeds and more or less relies on the single emotion of envy. This, and witnessing Dragon!Envy chomping down on Hohenheim, all of Hohenheim's blood gushing out and then dripping out of Dragon!Envy's mouth...Brrrr....'
Envy and Hohenheim in the movie. Especially the whole hanging up there, having something pierced through your body, waiting for finally something to happen... Highly unsettling, especially considering the time period Hohenheim hung there in Envy's mouth!
The expression on Mustang's face as he is ready to kill himself in the Ishval flashback episode is nothing short of haunting.
Barry The Chopper. Unlike in the manga/Brotherhood anime, his sadism is not only played seriously. It's terrifying. In episode 8, he kidnaps both Winry and Ed. He has Ed tied to a chair with his automail arm taken off and has Winry Bound and Gagged. He graphically talks about how he likes slicing people into pieces and makes several Nightmare Face's. He slices Ed's arm and mentally tortures him while trying to murder him. Seeing Ed crying and screaming makes it especially bad.
Martel's death. It's roughly the same as in the manga, but the most major difference is that the actual killing is shown from Al's point of view. Also, Al told her to hide in his armor to get away from Bradley/Pride.
The way Greed's body contorts when he dies. His eyes are bulging, his skin is dried up, and his mouth is agape as if he wants to scream but can't. Ed's scream of agony as his dissolving body sinks into the floor makes it all the more chilling.
Hughes's death is only a little different in this version, but in a way that largely changes the atmosphere. The part with Lust is mostly the same, it's when Hughes goes to call on the phone in the lobby. The random girl he runs into is replaced with the Fuhrer's secretary, who is the anime's version of Sloth, who also tries to kill him. It gives it a kind of Paranoia Fuel feeling, like the homunculi can be anybody and anywhere, and there's nowhere to run.
That horrible thing that Ed and Al made when attempting to revive their mother? It lives on and eventually becomes Sloth.
At the end of the series, Gluttony attacked Dante and she tried to transmute him to defend herself. He ate her before she could complete the transmutation. This could be insinuated as being the result.
Scar's older brother is revealed to have suffered Sanity Slippage. The combination of his lover's death, failing to revive her through human transmutation, and the imposing threat of a war on his home eventually pushed him over the edge. Using his own body, he planned to create a Philosopher's Stone out of Ishval's people during the massacre. He wandered out onto the battlefield completely naked with Ax-Crazy eyes and tears streaming down his face as Scar watched in horror. It didn't end well.
Not to mention the reason he was naked; the sacrifice he made for human transmutation to bring back his lover/Lust? It's strongly implied to have been his own genitals. OUCH.
Eckhart and her Thule Society mooks in the movie crossing the Gate over into Amestris...and subsequently getting themselves transformed by whatever the hell's in there. The viewers could even see said mooks practically screaming as the Gate morphs them. When Hughes shoots a heavily mutated Eckhart on the return trip, it comes across as a blessing.