The ending. Just about the last ten minutes of the film is one long string of happy, but the best part is when Ponyo flips out of the bucket in her little bubble, she and Sosuke kiss, and she turns into a real human girl. The last shot of the movie is a freeze-frame of her happy face.
When the old ladies are shown to be able to walk again, and are racing each other across a field. They're just so happy.
The morse-code scene, where Sosuke's father tells his son "I'm sorry and I love you" becomes a lot nicer when you learn about the Reality Subtext. That was a message from Miyazaki to his son.
"Ponyo loves Sosuke!"
Fujimoto is human in appearance only, and basically every action he makes draws attention to how completely inhuman he is. However, it's finally shown that he truly does care for Ponyo, very deeply, and is only trying to make sure both her and the world are safe. A surprisingly complex character for a kid's movie, and probably why he's an Ensemble Darkhorse.