Bebop and Rocksteady shooting the Michelangelo clones with their laser guns in Shredder's hideout.
Rocksteady: Just like a shooting gallery! Bebop: Yeah, it's times like this I wish I could count so I could keep score! Shredder: Stop, you idiots! You'll hit something! Bebop: Yeah, like turtles!
Bebop and Rocksteady think Shredder is a "toitle in disguise".
Shredder:(seeing his synthesizer destroyed) What happened to my beautiful synthesizer?! [Bebop and Rocksteady jump on him] Bebop: Great disguise. Rocksteady: Yeah, but not good enough to fool us! Shredder: Ahh, you idiots! What are you doing?!
Shredder whining at the end of "Shredded and Splintered"
Shredder: But I don't want to conquer this place! I want to conquer Earth!!
Vernon upon seeing the giant Krang in his robot body in the same episode:
Vernon: Ugh, his brain is in his stomach...
When the street sweeper come towards them in "The Incredible Shrinking Turtles".
Some of Bebop and Rocksteady's bickering in "Super Rocksteady and Mighty Bebop" can be pretty amusing.
Rocksteady: Easy, Bebop! You're gonna make me drop this thing!
Bebop: I can't help it, Rocksteady. Lightning gives me the willies?
Bebop: Give me the disk, Rocksteady.
Rocksteady: Uh-oh! It ain't here! I must've dropped it?
Bebop: You twit! Now we're gonna get it good.
Of course, the whole episode in general is riddled with funny moments, from the mesmerizer making everyone act like a child to Donatello reprogramming Super Rocksteady and Mighty Bebop to dance and then self-destruct.
Rocksteady: I didn't study anything. They studied me!
This gem from "Bebop and Rocksteady Conquer the Universe, where Shredder and Krang have been affected by the Anxiefier, a ray gun that makes people afraid of everything they see:
Krang: I could use the computer to analyze the atmosphere's atoms for a cure, but there's one problem.
Shredder: What is it?
Krang: I'm too scared to touch the computer!
From "Planet of The Turtleoids":
Raphael: If he starts singing, I'd advise you to change the channel.
Krang's android body wearing a Modesty Towel and a shower cap. Much funnier than it sounds.
The main character of Leave It to Beaver as a freakin' mobster in "The Great Cufflink Caper".
In "Turtle Tracks", April can't tell the Turtles apart since they're all wearing trenchcoats and hats.
April: Nice going, Raphael! Only half the people saw you! Leonardo: I'm Leonardo. April: Oh, sorry.
Raphael: April, why would people make themselves look weirder than they already? April: I have no idea, Michelangelo. Raphael:I'm Raphael. April: Oh sorry.
Donatello: Uh, April... ? April: Yes? Donatello: Why would people wanna make themselves deaf? April: I really haven't a clue, Leonardo. Donatello: I'm Donatello. April: Sorry!
In the episode "Blast From The Past" the ghost tells Shredder that in order to prove he is the original Foot Clan sensei he must perform the dreaded "Cur-Li Maneuver" he makes it clear he doesn't know it, later Splinter after regaining his memory demonstrates it, it consists of dancing around his opponent going "woo woo, woo" like Curly from the Three Stooges, slapping his opponent and bonking them on the head going "nyuk, nyuk, nyuk".
Shredder: Why is it that whenever they do something wrong they're my stupid mutants?
Shredder being turned back into a child at the end of "Leatherhead: Terror of the Swamp."
Shredder: Krang, I need to grow up! Krang: That's what I've been trying to tell you for years!
The Elvis aliens in "Burne's Blues".
In one episode, the Technodrome's generator problems have gotten so bad that the villains have to rely on pedal power. At one point, power begins to fail while Bebop and Rocksteady are on the surface. Shredder looks at Krang and says thoughtfully, "Krang, you look like you could use some exercise." One Gilligan Cut later, Krang in his android body is pedaling!
Shredder: Faster, baby! Feel the burn!
Krang: Never...let them...see you...sweat!
Some of the show's many, many animation errors are this.
"Gee, where's that Abe Lincoln guy when you need him?"
The episode "Shredder's Mom". The title alone is probably enough to make you giggle, but the episode must be seen to be believed. Highlights include Shredder's mom escaping from a retirement home for villains, Shredder's trademark whining when he bickers with her, and Krang seeming to have a crush on her later in the episode since she's much more competent than her son.
Though the Red Sky seasons were pretty dark, they still had a few comical moments. One episode had the Turtles try to find where Dregg plans to go and mistakenly find their way at an animal testing lab. Raphael muses that Dregg knows Santa won't give him the puppy he wanted for Christmas.
Pretty much any time Burne chews Vernon out.
Vernon: We need a trick question! What's a trick question?
Burne: Here's one. WHY DID I EVER HIRE YOU!?
In 'Return of the Shredder', Vernon shows Burne his report on 'attack dogs' in the city.
Burne:What?! You waste my time and my crew on some stupid little poodle? Out, out, out!
Vernon: Hmph! In France they're called "The pit bulls of par-ee!"