"You can FLY, you can FIGHT, and you can - *Peter crows*"
"Do you know what my happy thought was, Jack? It was you!" Damn it, brings tears to one's eye.
Even before Peter recovers his memories, he fights his fear of heights to climb the mast of Hook's ship in an attempt to get his kids back. This really makes Jack look like a Jerkass for claiming he didn't try.
Peter's view of Neverland.
A newly flying Peter Pan humiliates him the same way Rufio did when teaching him to swordfight. Later on Rufio takes the Pan Sword out in what appears to be a final showdown between them. However he does the next best thing: He bows down and presents Peter the sword.
Rufio: You are the Pan.
Something about this conversation:
Peter: Somebody give me a hand.
Hook: I already have.
Just the smugness in his voice makes this Hook's best line in the movie.
Smee gets one for giving Hook the plan to make Peter's kids love him.