This woman's face. Most people have seen the numerous dead bodies in this series without flinching, but this picture of a woman BEFORE death ...Just look, even though she's a bit demented, she KNOWS she's going to die. That expression on her face is nightmare fuel enough. While there're numerous dead bodies in the series with or without flinching, Mrs. Ayane's expression is so exaggerated that it actually plows straight into Narm.
Sunset Mansion. Ever wondered what it'd be like to see Lawful Good characters murder one another? They all live and are unharmed (save for the Hercule Poirot knockoff who was actually one of the two villains and was killed by the other one), but Hakuba and Kogoro with guns is something one doesn't want to think about. One has to note, though, if we believe in the Non-Serial MovieThe Fourteenth Target, Kogoro is actually a top-notch pistol marksman.
The Mountain Villa Mummy case, anyone? As in the one where the killer chops the victim to little bits and smuggles them into the forest one-by-one under his shirt, and attacks Ran/Conan with an axe in the middle of the night?
The murder from the very first episode featuring decapitation and High-Pressure Blood. Yes, this episode is the only one where the Japanese censored the blood.
Also, the case that takes place immediately after Heiji Hattori's introduction case -- the one where Conan and his three elementary school-age friends are stalked around the library by a psychopathic, drug-smuggling librarian who has no problem whatsoever with strangling them because they know too much? Not to mention his face during the whole time he was stalking them... in the dark.
The Rich Bitch Reika Yotsui's death in Billionaire Birthday Blues is simply made of this. She was actually bound and taped up inside a bathtub, with the cover placed over her....while it gradually filled up with water... and drowned her. And it happened in the span of hours, specifically to make Reika experience a slow and terrifying death, and it shows when her corpse is found with bulging eyes and an open mouth... meaning she was trying to scream for help for a long time, yet nobody could hear her. *shiver* While she is an Asshole Victim, but still.
In the manga, Shinichi's mental description of what's happening to his body while he shrinks sounds rather unpleasant.
Not that it's much better in the anime either. His train of thoughts as he shrinks for the first time is by the lines of "I feel like my bones... are melting away! MY BONES ARE MELTING AWAY! MELTING AWAY". Eeeeeew.
Massacre Night, if you do not know how the villain went about what they did, then you might be a little jumpy, because that can be done in real life too. The spelling out of Massacre Night and everything made the killer sound like a demented serial killer. And the characters are all stranded up in a blizzard.
The Mermaid Island case seriously freaks at least some troper out. Heiji and Kazuha, dangling off a cliff, Heiji only hanging on with one hand... and she stabs his hand with an arrow to make him drop her so he can still save himself.
A Cursed Mask Coldly Laughs. There's just something deeply unsettling about getting killed with your throat slitted by a knife, but it gets even worse once you consider the knife stabbed the throat. As in, it was pushed forward.