On opening night of the original play, the actress playing Peter questioned what she would do if, during the Clap If You Believe scene, the audience refused to clap. It was suggested that, should it come to that, the orchestra would provide the clapping. They needn't have worried - when that scene came, the entire audience erupted into a standing ovation, bringing the actress to genuine tears as Tinker Bell was revived.
After Tinker Bell (who has been jealous of Peter and Wendy the whole movie) risks her life to save Peter from the bomb:
Peter: Don't go out! Don't you understand, Tink? You mean more to me than anything in this whole world!
And even as she's fading away, Tinker Bell uses the last of her strength to tell Peter Pan that Wendy and her brothers are in danger, making this moment a near Redemption Equals Death for her.
Don't forget the end, with the family all watching the golden cloud-ship through the window, and Mr. Darling mentions having seen that ship before, a long time ago, when he was very young.
Also when you realise that this means that Mr. Darling himself was a Lost Boy once.
Even more heartwarming when the reprise of "You Can Fly" starts up with those suitable words: "When there's a smile in your heart, there's no better time to start!"
The scene near the end of "Return to Neverland", when Jane's renewed belief in fairies restores Tinker Bell to full health. Tink sees Jane crying, she smiles benevolently at the girl and gently tugs at her hair to get her attention.
In the second movie, when Peter sees the grown-up Wendy again.
Wendy: (Wendy looks out the window and Peter appears) Hello Peter.
Peter: (Peter looks away sad) You've changed...
Wendy: (Wendy smiles and turns his face to face hers) Not really, not ever.
The subtle love between Mr. and Mrs. Darling. Just look at the smile he gives her at the party!
Mrs. Darling's explanation of bravery to her children concerning their father.
At the climax, when Hook has left Peter lying on the deck almost beaten, Wendy asks if she can give him a "thimble" and then whispers to Peter, "this belongs to you, and always will" and kisses him. This of course sets off a Crowning Moment of Awesome for Peter.
At the end the children have come home and the father is restraining himself before letting go and showing how happy he is that the children are home. Also Slightly comes late to the house to find that the other Lost Boys have already been "adopted" by the Darlings. Aunt Millicent then gets some fairy dust blown at her by Tinker Bell.