The entire "Mango Juice" segment of the "Kon Ducki" episode.
Heck pretty much all of "Kon Ducki", especially the "making of" part with the Running Gag of Plucky's name being misspelled on his chair ("Ploogy Doog") showing how they did the "whirlpool scene" ("Go baby go!") and the revelation that Sweetie is actually Richard Nixon.
That wasn't a misspelling, it's his name with a really bad Scandinavian-ish accent.
In a scene from the episode titled "Animaniacs", we are given Gogo's... "unique" cartoon. It is so bizarre and unlike anything else in the series, that the audience (when shown watching the cartoon) have these hilarious facial expressions that just scream, Oh my God, what am I WATCHING???
Shirley the Loon's ending to her excruciatingly long cartoon. "Like, THE END ... fer sure."
In Starting From Scratch, when Buster tries to fight the bedbug with a homage to Bugs's Mexican hat dance. The animation combined with the music just sells it on a truly hilarious level.
Same episode, when Babs, Buster, and Plucky are inside Furball's head messing with his pleasure center and releasing his worst fear.
The Mynah Bird's cameos in Buster and the Wolverine. Especially when the characters land in a snowdrift after being spit out of the Wolverine's stomach and Plucky watches it walk off, saying "So that's what was jabbing me in the back!"
I forget the episode, but the heroes are in a mansion, and Babs starts swinging around the room on a curtain cord doing a Tarzan yell for no apparent reason. When she lands, Plucky just glares at her and says "That was unnecessary."
Fifi La Fume in the episode "Aroma Amore" has a few great lines but the best has to be after she gives herself a makeover she says to the camera "If looks could kill you would not be feeling so well, eh?" Also her calling the fleeing Furrball a flirt.
From thirteensomething, the two network executives Edward and Fran, who keeps telling him that he's "so lost". When Buster emerges on the show as Babs "long lost twin" we get this:
Edward: This is great!
Fran: You are so lost.
Edward: No dear. YOU are lost!
(Fran gets hearts in her eyes)
Fran: Oh Edward! Kiss me! (She lunges at him)
Plucky: (To Babs after she hits one too many berserk buttons) I'm naming my first ulcer after you.