Team Rocket provides most of the funny moments in the movie. Especially James' reactions to everything that happens, and Jessie's replies.
Jessie: What's all this?
James: Well, it's not my idea of decorating...
Jessie: Would you be serious?
- and a second, which is especially funny because he is right:
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!
- When their hot-air balloon is destroyed at one point:
- 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:
James: They're walking through the stream?
James and Jessie: Then they're WADING!