Quellcrist Falconer's fate after the attack on Millsport at the end of the Unsettlement: her body vaporized, and her mind trapped in a Martian data storage system for three hundred years. One of the downsides of having the technology to back your mind up somewhere.
The Qualgrist Protocol from Woken Furies, a bioweapon from the Unsettlement developed by the Quellists that uses Genetic Memory coupled with a symptomless virus to create a pheromone-based biological response in anyone carrying the right genes who got infected, so that they are compelled to try and kill anyone with Harlan family genes. While the Unsettlement was an example of The Revolution Will Not Be Civilized, the fact that Nadia Makita ultimately deploys the Protocol while hallucinating and while she's unsure whether or not she's real ensures that the events following the conclusion of the novel will almost certainly be bloody and horrible.
All of Kovacs' hallucinations/memories of Innenin and the viral strike there, including but not limited to Jimmy DeSoto clawing out his own eye. Arguably, what makes this truly nightmarish is not the event itself, but the fact that Envoys are conditioned to have perfect recall and so can't truly forget anything they experience, even if they also have the conditioning to lock away trauma so it doesn't destroy their psyches.
The very real possibility discussed in Fridge Horror that all of the re-sleeving is really just cloning and brainwashing rather than a transfer of "you."
Takeshi Kovacs murdering the entirety of his former Wedge unit in revenge. The fact it's in revenge for the horrific mutilation and day-long execution of a friend only makes it worse.
