The comic book Raphael is reading bears a mark similar to the one used by the Comics Code Authority to denote comics with wholesome values. The Comics Code Authority (CCA) was formed in 1954 by the Comics Magazine Association of America as an alternative to government regulation; it lasted until the early 21st century.
The line "Well done, my pretties", spoken by Baxter Stockman, is a reference to the, often misquoted, line delivered by the Wicked Witch of the West when she sends her winged monkeys to capture Dorothy and Toto in the Wizard of Oz. Rather than saying "Fly, my pretties! Fly!", the witch actually says "Fly! Fly! Fly!"
The ringtone for Donatello's Turtlecom is an instrumental remix of the theme from the original Teenage Mutant Ninja Turtles (1987) cartoon series.
The name Stockman Industries can be seen on Baxter's desktop wallpaper.
The name "Irma", along with a shot of the glasses-clad eyes of a young female, appeared on the caller ID of April's cell phone before it breaks. Beneath her name, it seems to read "Weirdo McGee". In the original Teenage Mutant Ninja Turtles (1987) cartoon, Irma was April's best friend, and both worked for Channel 6 News. Irma also wore glasses.