The bird funeral when you realize that they're holding the funeral for the young lark when he's standing right behind them. I couldn't help but think that crossed the line twice.
Willy and Waggs commenting on the Flapper-Wingamathing.
Willy: (about the Flapper-Wingamathing) You don't really mean fly...
Waggs: You heard 'em, they'll flap their little paws and fly like birdies!
The end of the scene where the furlings break Cornelius's wingamathing model. A book drops on it. The title of the book? Gravity.
"Grrrreat Honk!" (or is it Hulk? Hawk? Hog? Someone help me out here).
The captions say "honk", not that it makes any more sense.
Willy saying that he hopes Abigail wasn't hurt when she threw him out of the tree (actually accidentally dragged him down and then landed on him to boot). A different delivery would have made the line sarcastic or passive-aggressive, but Willy sounds so sincere in his concern that it's worth a chuckle.
Russel and Edgar are climbing up to the owl's nest to save Abigail, and at the same moment she frightens the owl so badly that it accidentally blows her out of the nest flapping its wings. This exchange follows: