I've been replaying for the first time and so far my worst moments were Kirin's blackmail, Molly's scene, Maya's scary room, Maya's flashback during the reset to bring back summer, Tsuneyo's stand up routine, Nodoka's blackmail, and rapist Makoto.
Most emotional moments were Akira and Rin's first kiss, Ayane fighting Kirin back, Maya receiving the scarf, Ami hugging Makoto in class, Kaori saying friend for the first time, Chika's mother looking at their house full of life from the portrait, Yuki's talk with Yumi after the Nodoka's events, Akira's first flashback through Niki's letters.
But really, almost all events are much better on a replay, you pick up on so much more stuff. I just wish we didn't have to play printscreen with flashing images and mess with wiki's and hexadecimal and online cipher translators just to understand what's written on the screen.