This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Orphan Black
Beth's suicide by train is very graphic, and we get to see the effects on her in detail.
Helena. She is very disturbing.
The rebar scene. God, that looked painful. The web of scars on her back don't help.
And when she's pulling it out with her blood and guts spilling everywhere in the opening to episode four. Even more terrifying when you remember that a little boy was present and she covered him in her blood. He later called her "The Angry Angel".
The fact that she doesn't do a clean, tidy job in fixing herself up, either. When she turns around, we can still see the rebar wound bleeding even through the stitches, plaster and shirt she's wearing. That's a way more realistic approach to the idea of patching yourself up than we usually see.
She also cut off Olivier's tail.. and danced with it. Yes, he's a bad guy, but still.
A lot of the "enhancements" made by the neolutionists are highly disturbing, most notably Olivier's tail.
By the way, human cloning has progressed much, much further than you think it has. You could be a clone and not know it. There may be ten different people genetically identical to you walking around right now, and you're all being monitored by a shadowy organization of scientists who break into your house at night and conduct tests on you with the connivance of the people you love and trust. Sleep well!
Sarah's non-nightmare about Dr. Leekie's people performing tests on her are extremely unsettling.
Hot melt glue to the chest. Ow.
Aynesley's death (getting strangled by having her scarf stuck in a sink grinder). To make matters worse, she wasn't even Alison's real monitor!
Amelia's gruesome demise. She shows up at Beth's house and Helena stabs her. Sarah then arrives home to find a huge blood stain on the carpet. She goes down to a warehouse and there's Amelia, beat up and tied to a post with chunks of her torso missing and bleeding from her mouth and abdomen. She went out suffering.
Helena and Sarah's confrontation. Helena shows up with a flare, which gives her a demonic glow, then proceeds to beat the ever loving crap out of Sarah, nearly strangling her with a huge chain. Sarah grabs a gun and shoots her.
Helena survived the gunshot. In the first shot of her in season 2, she's staggering into a hospital, just gushing blood.
The horrified admissions-desk nurse who sees the bloody Helena stagger up to her, mumble "Excuse me, my sestra shot me," then collapsing, is is probably gonna need a TON of therapy.
Hank's branch of the Proletheans are apparently going to try and impregnate Helena. This is horrifying enough but it crosses into squick territory because Helena has been shown to have the mentality of a child at some points.
The squicktastic "wedding" between Hank and Helena. Not only is there the fact that Hank is probably twice her age, but he also most likely plans to impregnate her. Helena is also pretty much catatonic throughout the whole thing, giving it a distinctly rape-y vibe.
Helena escapes and finds her way into Hank's breeding lab, where she starts having flashbacks of having been medically examined while drugged semi-conscious.
The very idea of Helena being forced to conceive. She can barely take care of herself, let alone a baby. Not the mention its practically a case of Child by Rape since her ablity to give consent was taken away.
Helena being the one shown to have killed Daniel. She's blood-soaked, in a wedding dress, holding a knife and wearing a creepy expression throughout it all.
In addition to being pretty scary for the viewer, this must be truly horrifying for Sarah. Here she is, already inches away from death and then she sees someone she thought was dead- someone she killed herself. Helena approaching her and laying her head against her as the scene ends with Sarah crying is frightening to watch.
Everything that happens to Grace in Ispa Scientia Postestas Est. She has her mouth stitched shut by her parents for refusing to tell them what happened between her and Helena. Eventually she does, at which point they tell her that if she doesn't help them get Helena back they will force her to carry Helena's fertilized eggs.
While we don't get to see much of them, the archives of the Cold River experiments give not only Sarah, but also the viewer, the creeps. There is one chilling photo of an infant labeled "Perfect Baby", followed by countless sepia-toned images of deformed fetuses and prototypes gone horribly wrong. The archivist herself tells Sarah that what she sees in them won't leave her.
It is finally revealed that although Helena will not be made to carry any children, Gracie was actually impregnated with her eggs against her will. The truly disturbing part is that they were all fertilized with her father's sperm.
At the end of Things Which Have Never Yet Been Done, Helena discovers Hank's plans to mass produce children using her eggs and his sperm. How does she get revenge on him? By stabbing him in the groin with a giant artificial insemination gun (essentially a long, slimy and pointy pole) while laughing maniacally.
In Things Which Have Never Yet Been Done, Rachel's breakdown while watching the Happier Home Movie of her and her parents is as tragic as it is utterly terrifying.
In By Means Which Have Never Yet Been Tried The clinical way DYAD interrogates Sarah, forces her to strip while she talks about the most intimate and private moments of her life and then, later in the episode forcibly straps her to a gurney wheeled into an operating room and tells her their plans - that they are going to remove one of her ovaries for experimentation. And that's just the first day. Later they plan to impregnate her (make her a brood mare as Helena would say). Here we get a truly terrifying glimpse at what exactly it means to be owned by DYAD
In the series finale Sarah is taken down to a lab where she (and the audience) are showed that there is a male set of clones , just the way one of them with a long scar running from his temple down his cheek to his chin and breathing against the glass.
The lovely shot of Dr. Nealon performing eye surgery on Rachel. And later Delphine pressing down on Rachel's socket to torture her for information.
Ferdinand in general, especially when he's getting way to close for comfort with Alison.
Alison and her family were one text message away from being burned alive in their home.
Seth brutally beating up Mrs. S. and shooting the security guard in the back of the head.
Helsinki: Rachel and Ferdinand had been secretly eliminating clones and their loved ones.
Rudy and Seth's rape of Patty is bad enough in itself, but its framed in a really creepy way and initially she doesn't even know there's another man in the room. Imagine having a nice time with a handsome guy, then out of the blue he decides to "share" you with his brother, who apparently has been watching the entire time. No wonder she's so shaken afterwards.
The graphic detail of Miller and his fellow soldiers water-boarding Helena — who is pregnant.
Seth's "glitching" is disturbing to watch. It gets so intense that Rudy puts a bullet in his chest out of pity.
Turns out Gracie's mother Bonnie is horrifying when angry — particularly when she shoots Mark for his betrayal, and later when she blames Gracie for her miscarriage.
Helena finds a Castor clone being held against his will during her escape. She pulled off his cap to reveal that his entire scalp had been removed and wires were going directly into his brain. He then begs her to kill him and she obliges out of pity.
Felix's Beware the Nice Ones moment with Rachel. Even with everything Rachel did, it's quite unnerving to see him gleefully tormenting a helpless, brain-damaged woman.
Delphine's interrogation of Shay is fairly unsettling, especially when Delphine tells her about a girl she knew who attempted suicide by slitting her wrists in the bathtub... while drawing a bath.
Dr. Nealon attempting to spit that freaky worm-thing into Delphine's mouth, and then it crawling back inside him when he died. Gross.