In earlier episodes, these villains always seemed to be defeated by a rush of water as seen in New Friend, Old Enemy, Never Say Xever, and The Gauntlet, but in The Gauntlet, Chris Bradford & Xever were flushed down by Mutagen.
Michelangelo, Naming Master - Michelangelo has given names to nearly all of the villains and gadgets on the show and was visibly angered when the Rat King named himself.
me - At least once in every episode Stockman appears in, his name is butchered, either by the turtles or other characters. Favorite mispronunciations include: Dexter Speckman and
Face Palm!
Boxer Stockboy.
Leatherhead grabs Donatello by the face - In both of the first episodes where Leatherhead has appeared, It Came From The Depths and TCRI, he has angrily grabbed hold of Donnie's head during one of his rages.
Kung fu frogs - Every time the turtles encounter Spider Bytez, he always thinks they are frogs and that they use Kung Fu instead of Ninjutsu. Hence, he calls them "Kung fu frogs".