* Doppler trying to convince the robot cops to let Jim go:
-->'''Doppler''': Excuse me, uh, officers? Perhaps ''I'' can be of assistance. I am the famous Doctor Delbert Doppler. Perhaps you heard of me? ''(Uncomfortable {{Beat}})'' ''No?'' I do have a clipping...
-->'''Cyborg Cop''': Are you the boy's father?
-->''(Both Doppler and Mrs. Hawkins react very squickily to the suggestion)''
-->'''Mrs. Hawkins''': He's just an old friend of the family.
-->'''Cyborg Cops ([[HiveMind In a unison]], booming voice)''': '''''BACK OFF, SIR!'''''
-->''(Doppler winces in reaction)''
* Jim's confrontation with Scroop.
-->'''Scroop''': Maybe your ears don't work so well.
-->'''Jim''': (''squicks'') Yeah. Too bad my nose works just fine.
* And the priceless scene between Doppler and Amelia after Doppler strikes his target perfectly with his gun.
-->'''Amelia''': Did you actually ''aim'' for that?
-->'''Doppler''': You know actually I '''did'''?
* "[[ShoutOut Dangit]], [[Series/StarTrekTheOriginalSeries Jim]], [[ImADoctorNotAPlaceholder I'm an astronomer, not a doctor!]] I mean, I am a doctor, but [[NotThatKindOfDoctor not that kind of doctor]], I have a doctorate, it's not the same thing, you can't help people with a doctorate, you just sit there and you're ''useless!''"
* Morph imitating Captain Amelia in a high-pitched voice, when she says [[GettingCrapPastTheRadar "Spaceport floozies"]], adding in a sort of hip-wiggling movement.
* Jim chasing Morph. This one's sorta debatable, [[MoodWhiplash considering the two scenes this one is set in between.]] But if you watch it in freeze-frame (aka repeatedly pausing), just ''try'' not to laugh at Jim's flying pounce.
** 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!"
* "Spider-psycho! Spider-psycho!"
** "A little uglier." "Nyahahaha!" "Pretty close."
* B.E.N.'s life is flashing before his eyes, and it's ''hilarious'':
-->'''B.E.N.:''' Jimmy, II don't know about you, but I'm starting to see my life pass in front of my eyes. [[LaserGuidedAmnesia At least, I think it's my life...]] [[NoIndoorVoice WAS I EVER]] [[NoodleIncident DANCING WITH AN ANDROID NAMED LUPE?!]]
* "I am ''not'' leaving my ''buddy'', Jimmy!" (One DeathGlare 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 [[ThrowItIn 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.
** [[FridgeBrilliance Jim brought a pet home at the end of the movie:]] ''Morph''.
* "Disable a few laser cannons, what is the big deal? All we gotta do is find out one little wire- *cue tangle of wires* [[OhCrap 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!"
-->'''Sarah:''' Now, at last we hear some sense.
-->'''Doppler:''' That's why ''I'm'' coming with you.
--> '''Sarah:''' DELBERT!