- The end of the six-on-six battle between Ash and Lisa, with Pikachu and Quagsire bonking heads with each other.
- James' line about the strange letters he received after placing a personal ad.
- Not to mention his incredibly girly yelp after he face-plants on the stairs and his reaction to the Unown: "Oh no, what now?"
- Team Rocket provides most of the funny moments in the movie.
Jessie, James and Meowth: TEAM ROCKET'S-!! (balloon crashes)
- When their hot-air balloon is destroyed at one point:
Jessie: What's all this?James: Well, it's not my idea of decorating...Jessie: Would you be serious?
- James' reactions to everything that happens, and Jessie's replies.
James: It looks like a storybook land, invented by a five-year-old!Jessie: That's ridiculous, James! Just keep running, and leave the thinking to me!
- A second, which is especially funny because he's correct:
James: Jessie, how can we breathe underwater?Jessie: Just go with the flow, James. Sometimes it's better not to ask questions.Meowth: I got a question I'd better not ask. You think we're gonna get a bigger part in the next movie?
- Then as Team Rocket swims through Molly's underwater illusion.
James: They're walking through the stream?Meowth: Yeahhh...?James and Jessie: Then they're WADING!
- The Who's on First? bit with Meowth wondering if the heroes are walking through the water, or they're waiting. It eventually gets to the point where James is absolutely fed up with the bit, leading to this:
- Entei running around a bedroom with a small child on his back while cheerful music plays is pretty funny. Not to mention adorable.
- Phanphy vs Onix: a Curb-Stomp Battle, but not the way you'd expect. The look on Onix's face◊ is priceless.
- The way Delia snaps out of her brainwashing—she sees Ash scaling the tower on the news and when he nearly falls she shouts "ASH KETCHUM, YOU GET DOWN FROM THERE THIS INSTANT!" Seems her urge to nag was stronger than Entei and the Unown's brainwashing.
- Somewhat easy to miss, but the expression on Ash's face when Molly transforms into a girl about his and Misty's age.
Funny / Pokémon 3