Mr. Kurtzman's line "They found me, I don't know how but they found me" is Doc Brown's line from Back to the Future.
Slash makes a planet of the apes reference with the line "damn dirty ape"
The first scene where Donatello, Michaelangelo and Ice Cream Kitty are watching a bright explosion directly parallels the scene at the end of "The Lost Boys" where Sam and the Frog Brothers watch an explosion. In both scenes three characters are huddled together, two wearing goggles, while the third does not, and a bight light is reflected off their faces. Corey Feldman who played one of the Frog brothers is also featured in this episode as Slash.