Amaterasu jumping up on Waka and licking his face after the final boss fight. Positively adorable, and shows that Sun Goddess or not, Ammy's a Big Friendly Dog at heart.
To this troper, it's being on the Ark of Yamato and talking to the spirits of the slain Celestials, who are awed and overjoyed at seeing their goddess return after such a long time. While it's tearjerking in that they can't join her back to the Celestial Plain, the respect and love they have for Okami Amaterasu is palpable, and it's a big reminder of the benevolent goddess Amaterasu really is, despite her Cloud Cuckoo Lander ways.
When you use Veil of Mist during the final battle with Yami, Queen Himiko's spirit appears to give you some health, effectively helping Amaterasu out twice after her own death.