Pretty much the entirety of "Rocketh and Rideth". The best parts include the Biker Mice pretending to be the three witches from Macbeth and Limburger Plaza being beamed into the world of the Three Little Pigs, complete with Limburger, Karbunkle, and Greasepit as the three pigs with the wooden Limburger Plaza being blown down by the Big Bad Wolf.
Everything done by Fred the Mutant is pretty hysterical. Easily one of his most hilarious moments was in "Road Ravens" when Dr. Karbunkle revealed that he ate the counterfeiting machine Limburger asked Karbunkle to make.
In "Upwardly Mobile", High Chairman Camembert begins to tell Limburger what he'll do if he fails. Limburger proceeds to press the "Mute" button on the monitor while standing there and muttering insults to his superior through a feigned grin before turning the sound back on to hear Camembert yell "until you squeak!"
Charley tries to use the mice's catchphrase; however since she is on foot, it doesn't really works.
Charley: " Lets rock and… uhm… run?"
Also she really took the role of the Butt-Monkey in this episode, including falling twice in a pit full of mud and being stuck in a tire in Limburger's car ( only for her to roll out in another pit ).
The speeded up version of the Plutarkian greeting, since the High Chairman was busy.
Limburger decides to pilot the rocket personally after Jet Blaster is defeated. He clearly doesn't know what he is doing, leading Karbunkle and Greasepit to secure themself with a dozen safety belts each.
When the launch fails Limburger orders Fred to use the manual takedown, which consists of lighting up some fuse manually, burning up whoever tries it. Of course the little masochist freak is overjoyed.
Vinnie at one point mistakenly shoots down a flower cart, which results in him getting punched in the face by an old woman.
In the end, the Biker Mice and "Asphalt" Jack McCyber defeat Limburger by using the virtual reality ray to trick him into demolishing Limburger Plaza.
"Back to Mars"
Charley doing an imitation of Greasepit saying "Mr. Limburger ain't gonna like this".
Vinnie and Dr. Karbunkle fighting over the doctor's makeshift teleporter like a pair of toddlers fighting over a toy. They both repeatedly scream "Mine!"
"I, Greasepit"
Greasepit's disappointment at not getting to do the traditional Plutarkian greeting.
Fred the Mutant pouting after the Biker Mice throw him out of his plane with a parachute.
In "Biker Knights of the Round Table, Part 2", Merlin conjures the face of a gorgon while preparing to get even with Karbunkle for knocking him off his feet earlier. Karbunkle's response is "No, not my first wife!"
"Diet of Worms"
Lawrence Limburger, One-Eyed Jack Monterey, Gerald Gruyere, and Gutama Gouda doing the traditional Plutarkian greeting with four miniature holograms of Lord Camembert, who all get squished together by their butts.
Limburger, Monterey, Gruyere, Gouda, and Camembert whooping like The Three Stooges when they try to get away from the Biker Mice's explosives at the end of the episode.
In "Hickory Dickory Doc", we have Charley who, clearly in desperate need of some female friends, is having a pretty deep conversation with a (presumably) female Brachiosaurus about gender roles. No, we are not making this up.
In the same episode when Throttle sees that the baseball field has vanished he asks his bros if they had been playing the game with bombs… again.
In "Road Ravens" Vinnie and Modo (both with casts due to a previous accident) are driving a truck as a bait. Modo, to pass the time, write this on Vinnie's cast:
"To Vinnie, who broke his arm trying to pat himself on the back!"
We then discover it was in revenge to Vinnie writing this on Modo's cast (with a permanent red marker, no less):
"Get well soon, from your hero Vinnie!"
Then they both hit each other with their casts.
Caveat Mentor": Limburger's fame as a screw up clearly went well beyond Earth: when the two guards chasing Stoker explain how fugitives make them look bad, they add that is a situation he can well relate to.
In "The Pits" the mice stop a bank robbery: the leader of the thieves then threatens them saying he has a hostage.
Also, the robber threatens to burn him alive if the mice didn't surrender. Vinnie simply shrugs and starts to walk away (only to be stopped by Throttle).
"Unforgiven Cheese": When the battleship Limburger tried to steal is about to crash on land Charley, who is on the shore, proclaims she's going to stop it… only to look to the camera, admit "Right! Who am I kidding?", and run away screaming.
"Where No Mouse Has Gone Before": Every four year the High Chairman chooses an adversary with no chance of winning to run against him for the election, only to kill him after his inevitable defeat. This time his choice is Limburger who, rightly worried, starts having a panic attack during his presentation… acting exactly like a fish out of water.
Really, how everyone on Plutark is okay with how much of a joke this process is: at one point the winner is called "democratically elected dictator".
After their bikes got under the control of the Mechanic in "Vicious Cycles" the Biker Mice are forced to go after them on three brightly colored, girly scooters. It's a funny moment even In-Universe, since Limburger and Karbunkle had to lean against each other or roll on the ground laughing.
The Once per Episode gag of Limburger Plaza (or wherever he's operating from this time) getting destroyed in some hilarious way. Some instances can be seen here.
Possibly the most ridiculous instance was when a test tube containing the concentrated smell of the Loogie Brothers broke on it: the tower wasn't destroyed, it grew legs and ran away from the stench.
It didn't just run away, it ran straight into the bay in an attempt to wash out the stench.
In "High Rollin' Rodents" the Biker Mice destroys Limburger Plaza at the start of the episode. Cue the scene of it starting being rebuilt, with a sign announcing it's being rebuilt for the 54th time being corrected into 55th. For the rest of the episode Limburger operates out of a casino, that the Biker Mice blow to sky high... And then it lands on the just completed Limburger Plaza right after the foreman declared it completed. The foreman then replaces the 55 on the sign with a 56 and faints.
2006 series
In "British Invasion", when Stoker transforms into a monster and attacks the villains, Ronaldo Rump is the last one standing until his weight causes him to topple over like a bowling pin.
In "Biker Mice Down Under", Vinnie and Rump argue over which of them is a butt. Throttle says "I'd hate to interrupt this touching moment of immaturity", but then Vinnie and Rump both tell him to shut up.
In "New Cats in Town", Cataclysm gets so angry at Hairball for fouling up their latest attempt at defeating the Biker Mice that he repeatedly kicks him in the butt.
"It's the Pits"
After Modo compliments Limburger on looking slimmer than he did in the past (which is later revealed to be because he's wearing a girdle), Limburger then states that Modo should see him in a thong. Modo replies that he'll pass.
After getting hugged by the Pit Boss's daughter Twinkle, Modo remarks "Mama, what have they done to your son?"
At one point in "Break Up", Throttle and Carbine get lost in each others' eyes, resulting in Charley exasperatingly having to remind them that they are in the middle of a battle.
In "Swimming with Sharks", Vinnie responds to Modo asking him if his mother told him not to talk with junk food in his mouth by saying that hot dogs are not junk food, but the food of the gods. Immediately after he claims this, he gets indigestion and says "Or not."
The amnesia-struck Throttle in "Desperado" freaking out at the sight of Vinnie and Modo and losing it even more after he sees that he himself is a mouse.
Notably, Limburger finds it embarrassing and tries and avoids it whenever he can.