The scene where, during what may be their last night together, the girls are telling each other about how they'll always be friends. Also a Tear Jerker so sad, even the moon cries.
Madeline and Miss Clavel's reunion.
During the epilogue, Madeline's hair has grown back, but the rest of the girls have cut their hair in a similar fashion that LaCroque did to Madeline, most likely so she wouldn't feel ashamed of how her hair looked. Double heartwarming, they are proving to be Madeline's family in spirit by doing this.
The ending: Madeline donating all of her reward money to funding a brand new school at which her new friends from LaCroque's shop can finally have a real home. Doubly heartwarming is when Fifi reappears, cleaned up and healthy with her hair finally regrown.
Miss Clavel's unwavering dedication to her girls. Upon hearing that one of them (this one being Madeline) is missing, she rushes out to find her. Also, during her search, she finds Genevieve and lets her ride in the car despite her allergy flaring up around the dog.