The Shrike's Tree of Thorns, with its thousands of impaled humans being kept alive and conscious indefinitely. The fact that it's just a massive simulation and the victims are being kept under and alive via IV drip somehow makes it worse.
The little Bikura people (who'd been stunted by the prototype cruciforms) were quite frightening, especially before you knew what was going on.
What they did to Father Duré was pretty bad, though. Duré sharpened his arrestor rods and crucified himself, somehow missing the important blood vessels on his left arm. Normally, that should kill him, but he impaled himself on a Tesla Tree on the planet Hyperion. These trees release electricity, and since he impaled his arms and feet using metal rods with the Cruciform, they kept bringing him back to life. His clothing, skin, flesh were long-destroyed after seven years on the tree, but the electricity and the parasitic Cruciform kept him alive, constantly in excruciating pain. When his friend saw him and picked up his bestos bag and dropped the cruciform accidentally, it killed Father Duré. Just before dying, Duré smiled. This caused Hoyt to become so mentally and emotionally scarred that normal painkillers stopped working. He had to use Ultramorphine. He got better, becoming the pope for 200+ years.
Lenar doesn't need stronger painkillers because he's emotionally scarred - it's because he takes on Duré's cruciform and puts it on his back. Father Duré is still alive inside it - and when Lenar Hoyt dies, he takes over. That's right - every time the pope dies, he gets resurrected as his old mentor, who is immediately killed again to rise as the pope once again. Yeah, Father Duré has it hard.
Aenea's death scene. Go read The Rise of Endymion. Among other things, her fingernails are plucked out and one of her finger is bitten off by a clone of Nemes. She's half-blind, broken and nearly dead. She almost has her eyelids and nose chewed off by Nemes, and almost had her eyelids and lips sewn shut. Her feet are burned by a flame through a grate on the floor. She dies in the end, consumed literally by the fire. And the worst thing is anybody on a planet with someone who got communion from Aenea witnessed and felt what she went through. The same thing that almost drove our narrator insane.