'The Doctor Zone Files' is an amalgam of three popular science fiction television shows: Doctor Who, The Twilight Zone, and The X-Files.
In Rooting for the Enemy, Melissa says "Great Googly Moogly! This is a reference to what Major Monogram from Phineas and Ferb says.
In "We're Going to the Zoo", Vinnie Dakota loses a bet and must sing "We're Going to the Zoo" with pistachios in his pants. While singing, squirrels crawl into his pants and he says, "I've got squirrels in my pants," a reference to Phineas & Ferb and the song "Squirrels in My Pants."
Milo's pet dog is named Diogee. When spoken, the name sounds like saying the letters D-O-G.
In "We're Going To The Zoo", Milo's sister, Sara, asks Milo, "What happened to these platypus pajamas?" while holding up pajamas that look like Perry The Platypus and part of Perry's theme music plays. She also asks, "Why are they teal? Aren't platypuses brown?" Milo responds with, "Someone's idea of artsy."