The entire Butt Monkey sequence with Orville: first he's Groin Attacked by a firework, then gets his tailfeathers set on fire, causing a crash landing. When he tries to take off again, then he's sucked into Medusa's Swampmobile turbine intake, first with an all-bird sounding "squack!", followed by a Goofy Holler (water distorted, no less!) and an Ash Face once he's finally spit out the other end.
The entire calliope scene, especially Bernard's reaction to being shot up in the air and trying to run!
Fridge Brilliance kicks in when you realize that when Medusa hears the noise, her first thought is not 'Who is playing the organ?' or even 'Snoops, stop playing with the organ!' but 'ALLIGATORS, STOP PLAYING THE ORGAN!' Brutus and Nero must make it a habit.
Medusa: (storming out of her room) BRUTUS, NERO, STOP THAT INFERNAL RACKET! I MEAN NOW!
Even the music that plays as Nero and Brutus are walking is hilarious.
When Bernard talks to Orville over the radio, who first mistakes him for the ATC tower, then nearly gets blown away by a passenger helicopter taking off. After a bout of Angrish (completely with radio Sound Effect Bleep)...
Bianca: What did he say?
Bernard: I wouldn't dare repeat it.
The "preflight checklist" was hilarious. What does an albatross preflight? Goggles, wings, rudder ("tailfeathers"), and..."If at first you don't succeed, try try again."
Bernard: I wish we'd taken the train!
The Eek, a Mouse!! sequence that follows the calliope scene. It gets even better when Medusa starts firing a semiautomatic shotgun ... and everyone dives for cover from her erratic shots.
The entire charge of the swamp-dwelling Ragtag Bunch of Misfits is something straight out of a Three Stooges routine, especially when one of them sets off the fireworks on the boat.
Bernard: Advance the spark! (HONK!) Not the horn! The spark lever!
Anytime Luke (or somebody else) takes a drink of his Swamp Juice.
At one point, Penny does an imitation of Medusa's behavior, concluding with imitating Medusa's butt swinging as she walks! Bianca and Bernard found this funny in-universe.
The Rescuers Down Under
The whole scene when Joanna obsessively goes after McLeach's eggs as he tries to make an omelet as seen here. Particularly the end, where he seemingly outwits her and gloats.
"THESE ARE NOT JOANNA EGGS!"
this troper always thought it was humorously in character that he kept his eggs in a tool box.