Hell, everything after episode 34 inclusive is mainly Nightmare Fuel material, shown in this AMV. The images speak for themselves.
In episode 47, the entire mind rape sequence of Juri/Jeri, a 10 year old girl. And this is just a section of it; the actual mind rape has been going on, and will go on for weeks.
That Mind Rape induced flashback is enough to ensure people may never look at Jeri (and her handpuppet) the same way again without feeling uneasy or scared.
IceDevimon is all sorts of rape-y.
As scary as Dark Evolutions are, Megidramon definitely takes the cake. It certainly doesn't help that its name is derived from the words "Megiddo" and "Dragon", considering that Har Megiddo is the mountain, where the apocalypse is (according to the bible) going to start. Har Megiddo has later been given its more popular name, "Armageddon". In other words, Megidramon's name is closer to original idea of the end of the world than "Armageddon".
Dark Lizardmon's fate: It was captured by hypnos, interrogated under torture and literally torn apart for analysis while fully conscious after Yamaki was done, in a process that actually looks more painful than the equivalent, that is to say an autopsy on a living human. Not to mention that this is a close up to what shaggai/Juggernaut does to it's victims in episode 14.
An early warning of things to come, episode 14, where the screams of the Digimon deleted by Shaggai/Juggernaut can be heard. A tamer version of Homeworld cataclysm's corruption by the beast.