1. The weird tree face in the beginning? That's the Deku Butler's son. He mentions you remind him of his son, and the closing credits show him in anguish in front of the tree.
2. Pamela (the Daughter of the researcher turning into a Gibido) is a four (maybe six) year old effectively all alone and trapped because of the Gibidos circling her house, while the one person she trusted to keep her safe she had to lock into the closet.
3. The elderly Goron tribe leader is making his way to Snowhead all alone in the freezing conditions in order to try to console his son, despite being so frail he is constantly shaking and bent over nearly double.
And let's not forget the Anju and Kafei sidequest