Bebop's line "Turtles, come out and play-i-ay" in an homage to the 1979 classic film The Warriors.
When Bebop threatens Michelangelo with the retro-mutagen, he says "Time for the next mutation!" This is a nod to the short lived live action Turtles show, "Ninja Turtles: The Next Mutation".
In the "Crognard the Barbarian" episode Mikey is watching, Crognard yells "I have the energy!" This is a reference to the 80's show "He-Man and the Masters of the Universe", where the title character's catch phrase is "I have the power!"