And in the beginning of the same scene, Morph—who is now in the form of one of Jim's rough-terrain boots—winding himself up and literally kicking poor Jim's butt. Not even Jim himself could keep a straight face.
And then the little Whack-a-Mole game Jim does when Morph pops out of the grate as a miniature head of Jim saying, "You little squid!"
"A little uglier." "Nyahahaha!" "Pretty close."
B.E.N.'s life is flashing before his eyes, and it's hilarious:
"I am not leaving my buddy, Jimmy!" (One Death Glare later) "...unless he looks at me like that. Uh. BYE, JIM!"
"All my life, I've been waiting for an opportunity like this, and here it is, screaming: Go Delbert! Go Delbert!"
That part was actually improvised by David Hyde-Pierce.
A deleted line, when Jim's mother talks about how she had always dreamed of Jim opening the door with an animal he found, begging her to let him keep it. Then, the doctor opens the door to reveal Jim carrying a wounded Billy Bones.
Delbert: In the dream, was the pet dead?
In the prologue, there's actually a brief scene of a younger Jim holding up a strange alien pet, trying to get his emotionally distant father's attention.
"Disable a few laser cannons, what is the big deal? All we gotta do is find out one little wire- *cue tangle of wires* Oh, mama..."
"BACK YOU GO, YOU NAUGHTY PLUG!!"
And before they board the ship, Jim is trying to sneak through the pirates' camp and B.E.N. nearly gives them away, "SO WHAT'S THE PLAN??"
Jim hiding in the barrel of space-plums, nervously handing up Scroop one of them so that he doesn't notice him.
Doppler driving the ship, with Captain Amelia attempting to help him. "Attempting" being the operative word.
Captain Amelia: Go to the right! The right!
Dr. Doppler: I know, I know, will you just let me drive ?!
Even funnier, Onus screams, "We were better off on an exploding planet!"
When Jim theorizes about the whole planet being the mechanism and that the treasure is buried in the center of the planet, some of the pirates take him literally and begin trying to dig to the center of the planet.
Jim's mother turning to Doppler, expecting him to dissuade Jim from his idea of locating Treasure Planet:
Sarah: Delbert, will you please explain to him how ridiculous this is?
Doppler: It's totally preposterous! Traversing the whole galaxy alone!"