The Rain of Fire scene in Stoic's backstory. Also overlaps with Tear Jerker, since you know the peace doesn't last.
Stoic's memories of Dasani: first as he recollects at her grave about why he fought with her, and then as he recounts the story of her finding him.
Cade and Auburn's Relationship Upgrade. She still genuinely loves him, and was just as distraught as he was realizing that they, as Shroud and Sparrow, are enemies. She keeps her distance initially, but helped Stoic and the others rescue him when captured by the Hand. Cade later asks her if forgetting all about Equipment King, the Hand, their fights, what she really wants. Auburn wants to be with him, as proven by running over and hugging him.
A small scene, but when Bones wakes up from a nightmare, Cade also wakes up... from his bed where Auburn is also sleeping on, cuddling close to him.
Stoic finally making peace with the Robins.
Fairly minor compared to some other scenes, but the "once a Touten, always a Touten" scene, and all the moments that call back to it. Even though they might not always accept what he does, even though they may be against him on occasions, even though they should not have done it according to their own beliefs, they had accepted Shroud as one of them and one of them he will remain. Though they may not be together, they are True Companions of some sort to him, and that really counts.