Shinji comforting Misato during her breakdown after Vegeta’s painfully-truthful Breaking Speech, and then managing to bring her out of it.
Chapter 21, with Shinji & Yui talking in their mindscape, where Yui states how the AT Field is more than just a separating barrier: “It’s the light of our soul. Don’t you see, Shinji? The light of my soul… of my existence… is you”.
Nearly every interaction between Shinji and Rei:
Chapter 13: The adorable interactions as Shinji makes his decision on his feelings for the obviously-distraught Rei and embraces her; she’s so happy that she cries (bonus points for Fuyutsuki, watching from a room above, who decides to keep this a secret from Gendō)