While also listed as a Crowning Moment of Funny, this troper was a bit disturbed by the scene where the engineer is trying to explain the mecha problems. All these full-grown adults are coming up with ideas for a giant robot designed to kill thousands of people at the very least like little boys playing a game. There are similar scenes later on that have the same effect for this troper.
The few moments where Urasawa drew mysterious characters in a stylized ghostly art-style. Specifically Proffesor Shikishima's daughter in 21st Century Boys when she was shown in her creepy nurse outfit with those cold dead eyes.
Koizumi being forced to stay at Sadakiyo's house while he puts on his best Norman Bates impression.
The mere reveal that there was a third boy wearing a mask gave this troper chills. Mainly because of the implication that he had always been around, but we had just never known it.