The scene where she visits John Smith as he's imprisoned. "No matter what happens, I'll always be with you... forever." Cue heart-dissolving and lip-quivering from the sheer sweetness of that scene. It's even better accompanied by the deleted song.
Not to mention when they share their first kiss.
Meeko comforting Percy, when he's visibly traumatized by Kocoum's death, and setting aside their differences.
At the very beginning of the movie when a lot the male villagers are returning, the women and children are running to welcome them back. In fact, one of the women runs to a man and tackle hugs him so hard, they both fall back into the river. The chief smiled when he saw that for a reason.