Just about all of episode 9, Yuu's mother's wanderings through time-space. The whole thing really puts her previous behavior in context. Then watching Yuu and his mother smile at each other for the first time in the entire series was worth the wait.
When the amnesiac Atori sees Haruka crying for the unconscious Karasu. He walks over to them and tells Karasu kindly to please wake up so she won't have to cry any more.
Atori: What's the matter? You know you can't sleep now. The little girl is crying.
The ending of episode 20, when Yuu suddenly reappears after having faded away in Haruka's arms. Haruka rushes to him crying tears of joy, and even the stoic Karasu seems happy and relieved.
While Haruka's friends are trapped in Shangri'La, Noein forces them to experience a possible future that's very tragic. Haruka activates the Dragon Torque in an effort to free them from that horrible fate. The Torque sends Yuu to talk Future!Isami into saving Future!Ai. And Future!Miho is saved by Atori of all people. In the end they're all freed thanks to Haruka and Yuu's efforts.
Future Isami talking Ai out of killing herself is very heart-rending, considering in the present day he hasn't realized her feelings for him.
Isami: Even if you don't have your legs...if you wanna run, I'll run with you on my back! We can play soccer that way. So please...please don't do this, okay?
Karasu's and Haruka's final words to each other after the final battle near the end of the last episode.