"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.
Possibly the most Awesome lines in the movie, that capture the relationship between two Immortals who've been fighting for over a hundred years.
The lead up to it is just rife with awesome too with Rufio's death and deciding his children are more important than fun or revenge but ultimately acknowledging that Hook will never stop hunting his descendants and that he needs to finish things. The look on Hook's face when Peter walks away but then decides to fight equally captures everything that embodies the character.
Hook: Peter! I swear to you, wherever you go, wherever you are, I vow there will always be daggers bearing notes signed "James Hook"! They will be flung at the doors of your children's children's children, do you hear me?
Peter (slowly sets Maggie down, turns around) What do you want, old man?
Hook: Just you.
The crocodile coming back to life briefly after being stabbed by Hook and promptly eating Hook in one gulp. Bangarang.