"He hates humans! He keeps me in a bubble!" Ponyo, on her father.
Anytime Ponyo mentions HAAAAAAAAM!!!! Especially the scene when they're talking to Sosuke's father.
Sosuke: I'm taking care of everything, don't worry!
The Morse Code "Bug off/Baka" scene.
When Fujimoto is trying to explain to Toki and Sosuke that the entire earth is out of balance, he gets more and more flustered and starts flailing around. He seems so henpecked already, but then Ponyo wakes up and sprays him with water to shut him up. His reaction is to flail even more. "Brunhilde, respect your father!" He just sounds so adorably indignant, especially when he says, "Humans" and is so close to tearing his hair out.
In an early scene, he says the same thing, except to Ponyo's sisters, when they're pushing the wave he's standing on down. "Girls! Stop! Please! Respect your father!"
When Fujimoto is on land, trying to find Ponyo, and has a device used to spray water around. Lisa yells at him because she thinks he's spraying pesticides. Fujimoto indignantly gives a very bizarre explanation about how it's ordinary water he's spraying because he'll dry up on land otherwise, only for Lisa to basically say "That's nice, just don't spray pesticides" before driving off.
"I think I just saw the goddess of mercy!" followed by lots of frantic praying and bowing at the sea.