Dorothy: How can you talk if you haven't got a brain?
Scarecrow: I don't know! But some people without brains do an awful lot of talking. Don't they?
From that same scene, "Right! Tie my feet together..."
When the group is flying on the Gump to the Nome King's mountain, Jack sees the Wheelers following them and asks the Gump if he could speed it up. The Gump replies, "Not unless one of you wants to jump off!"
Jack: ...Tik-Tok, you're the heaviest.
When Mombi talks about waiting for Dorothy to grow a bit older before taking her head for her collection, Dorothy's response (made brilliant by Fairuza Balk's delivery).
Dorothy: I believe you will not!
When Dorothy and Billina notice the headless statues in the Emerald City.
Dorothy: They look like they've lost their heads.
Billina: Now that's just plain carelessness.
The Reveal of the Nome King wearing the Ruby Slippers is both funny and scary.