'The Girl in the Fridge'. The title reference is to a victim who was held captive in an old refrigerator and suffered increasingly worse pain because she couldn't turn over. And all the killers did was keep her quiet by giving her more and more drugs.
The murders of the girls in "Two Bodies in the Lab" - torn apart by dogs, amongst other unpleasant things. And the fact that it could have been Bones' fate at the end if Booth hadn't showed up.
"The Man in the Cell": The whole episode was downright scary.
"The Man in the Morgue" - the way it's shot, the way the murders are performed. All of it.
The Season 7 finale. An ever increasing exercise in paranoia.
Season 7, episode 2. The snake is hidden in the body, alive? Argh!!
PamNunan from "The Wannabe in the Weeds". Her stalking of Booth is deeply unnerving.
Considering the sheer variety of everything that happens to the assorted victims shown throughout the course of the show; pretty much every episode.
The boy at the beginning of "The Change in the Game": "Do you know what they do to little boys who are bad, even on their birthday?" ... cue the body of the week ...
"The Headless Witch In the Woods": The filming the victim made is straight out of a badly made horror movie but it works so much, Angela has to play rock music loudly so she doesn't faint from the screaming. In the film, there's also a thudding sound of an axe striking something, markings of the Witch's eyes strewn about the forest and at the end, Hodgins and Angela see something humanoid shaped behind the murder victim, looking a lot like the witch who supposedly lived there.