This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Bakemonogatari
See No-Holds-Barred Beatdown on the main page; Suruga's constant hysterical screaming of "HATE HATE HATE HATE HATE HATE!!!" while savagely beating Koyomi is quite disturbing. Good thing it was censored...
The fifth opening theme "Sugar Sweet Nightmare" is a bit unnerving. One scene in particular is when human hands burst out of the mouths of cats and roughly grope Tsubasa's naked body as she tries to run away from them.
There's also one of the final scenes in the last episode. The cat licks Koyomi's neck and his tongue is sharp enough to cause Koyomi to spout blood out of his neck.
The way the snake decides to attack Koyomi.
You tought Kanbaru's beatdown on Araragi was bad? The one he receives at the hands of Kagenui in the climax of Nisemonogatari is as terrifying as that one. Araragi is beaten so brutally he ends severely deformed (like if he was a zombie) and with a hole in his rib cage. See the results yourself to look how bad it is.◊
Kisshot's appearance at the end of Mayoi Jiangshi. She doesn't do anything particularly horrible onscreen but still, creepy.
The beginning of the Nadeko Medusa arc starts off with Snake God Nadeko stabbing Koyomi, whose body is already torn up from her previous assault, and giggling creepily in a shower of his blood. The entire arc is her descent into insanity.
The truth of Sodachi's mother's disappearance. Due to her mental issues, she was unable to admit to the fact her mother starved to death and thus spent two years caring for her corpse. Only once it decomposed beyond any recognition did she register her mother as "gone". Brrr.
The ending of Koyomimonogatari consists of Gaen calmly walking toward Araragi while talking about how to stop the darkness that engulfs the city... Before casually pulling the Kokorowatari and slashing Araragi into literal pieces that scatter into the air. And take note that this is a rare occasion where the series defy exaggeration from Unreliable Narrator because the narrator himself is in shambles now. This is what actually happening onscreen.
In Kizumonogatari II, when Araragi is being cornered by Episode during their fight, Hanekawa suddenly appears and tells him the weakness of the vampire hunter's mist technique. What Episode does to this? He attacks her with his cross and causes Hanekawa a wound so severe she ends with her guts spilling out of her body (in all its glory, without any kind of censoring like in the aforementioned fight of Araragi against Kanbaru). Fortunately for Hanekawa, she is healed before something worse could happen.
Araragi's Roaring Rampage of Revenge against Episode for this is not better either. In his wrath, he beats Episode so savagely that, if Meme wouldn't had appeared, he would had probably ended not only killing his oponent, but also losing his humanity.
In Kizumonogatari: Reiketsu-hen, we have this lovely scene of Araragi, excited to return to Kiss Shot for his celebratory farewell party with her after their sweet bonding moment just a few moments ago, walking in on her feasting on Guillotine Cutter's now dead body (guts and all). What makes this scene worse is how casual Kiss Shot was being with Araragi even as she shows him Guillotine Cutter's half eaten head by the hair in front of him, with Guillotine Cutter's head and body being rendered in complete CG to show just how unnatural the scene was. Araragi throwing up afterwards is an understandable response to the whole thing.