- 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. Not only does he care strongly for his daughter, he also has a soft spot for Sosuke as well since he clearly doesn't want to hurt the boy; he's just an Overprotective Dad who wants his daughter to be happy and safe. A surprisingly complex character for a kid's movie, and probably why he's an Ensemble Dark Horse.
- For the little time they interact, it's clear that Fujimoto and Granmamare are very Happily Married and their closeness isn't affected at all by the distance. Just his happy smile when he sees her approaching (the only time we ever see him smile) speaks volumes about the relationship between the two. Then there's the way she looks at him like he's the most precious thing she's ever seen, holds his hands and calls him "dear" and "darling," and is able to calm him just by touching him.
- Then there's his Adorkable bustling about his home after summoning her, even stating, "The thought of seeing her again, my heart is pounding!"
- Another thing to note in the reunion with Fujimoto and Granmamare is how he calls Ponyo by her new name rather than Brunhilde. Not only does Granmamare find the name absolutely darling but him using the name does show that he's starting to come around to Ponyo's choice of becoming a human. The only thing that truly terrifies him aside from the world flooding is that Fujimoto doesn't want his precious daughter to turn into seafoam but Granmamare is able to calm him down and help him believe in The Power of Love between Sosuke and Ponyo.
- The closeness between Lisa and Sosuke, and how Sosuke actually mediates between his parents and seems to understand both of them without resenting them.
Heartwarming / Ponyo on the Cliff by the Sea