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.
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 insulting his superior through a feigned grin before turning the sound back on to hear Camembert yell "until you squeal!"
In "Virtual Unreality", Vinnie at one point mistakenly shoots down a flower cart, which results in him getting punched in the face by an old woman.
"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 invention like a pair of toddlers fighting over a toy. They both repeatedly scream "Mine!"
In the episode "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 immature argument", 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.