Pretty much any of the confession scenes, but especially Haruka's and Kurumi's, both doubling as a Crowning Moment of Awesome for Makoto.
Haruka: Makoto not only confesses to her, but manages to get rid of the two problems that have plagued Haruka her whole life- that she has no "heart" and that she's nothing more than someone's replacement. This result in Haruka's Cry Cute moment.
Kurumi: Makoto, trying to convince Kurumi that both of them have time travelled at some point in their life, is asked for proof on his end. He recites Kurumi's dream (which she only told him about in the first loop) word for word, shocking Kurumi as they kiss.
The ending of Haruka's Route: "Goodbye... Goodbye... my sisters! We'll meet again..."