- The most obvious would be the worst material surrounding Asuka.
I was afraid. I took her out because she could have ended up like that: Having her soul sucked out of her through the back of her neck!
- In the same vein, Sohryu's realization of how badly she's screwed up in an attempt to protect Asuka.
- Mari's temporary death, and Uri's reaction to it.
- The last remnants of Naoko's soul being impaled by Iruel while Shinji watches.
- The "Iruel Mind Rape" scene is equal parts this and horror, especially what he does to Asuka, Mana and Ichi.
- Chapter 40: Kyoko, already distraught over learning of Asuka's Split Personality issue, is sent to the canon!Evangelion verse alongside Asuka, Shinji, Rei and Yui. Soon after arriving, she discovers exactly what happened to canon!Kyoko and how it affected canon!Asuka, and...well, her first reaction is to scream helplessly at how much worse she could have screwed up with her daughter, and afterwards she starts throwing wine bottles at Canon!Unit 02, screaming at it for its actions.
ND!Kyoko: What did you DO TO HER?!!
- Chapter 45: Yui has to ask Ichi to give up a paradise made for her to go back to being an Eva.
"It's alright. We had today, didn't we?"
- Makinami refusing to acknowledge Mari as her daughter because her Near-Death Experience turned her into a human/Angel hybrid. And I thought pre-Character Development Kyoko was bad...
- What makes this worse is that Pieter had reassured Mari that she was still herself and that he still loves her almost immediately beforehand.
- All of what happened in New Vegas after they left the convention. It's more like 2-3 chapters of tearjerking material than a moment.
- 02-Ef's "death" in Six AIs One Continent.
Tear Jerker / Nobody Dies
While Nobody Dies is, overall, very funny and a Lighter and Softer take on Neon Genesis Evangelion, it has its fair share of emotionally wrenching scenes: