In "Beyond the Sky", Sue's car battery cuts out as the alien ship is crashing, in much the same way as Dr. Clayton Forrester's watch stopped working when the Martian ship crashed in The War of the Worlds.
In "Jacob and Jesse", Eric and Sam pretend to be the space hero Captain Video and the Atoman dictator Vultura, the protagonist and main villain respectively of the 1951 serial Captain Video: Master of the Stratosphere which they have just watched on television.
In "Acid Tests", when Dr. Powell mentions Daffy Duck as an example of The Trickster archetype, Daryl says that Daffy once painted a white stripe on his back to disguise himself as a skunk. Powell points out that it was Sylvester who had the paint on his back and it was an accident. This occurred in the 1954 cartoon Dog Pounded.
Also in "Acid Tests", after the mummy disappears, Sarah wonders who was responsible. Buzz jokes that it was brought back to life by tana leaves. The mummy Kharis was revived using tana leaves in the Universal Horror films The Mummy's Hand, The Mummy's Tomb, The Mummy's Ghost and The Mummy's Curse.
In "Charlie and Lisa", Dr. Wakeman says to the Joint Chiefs of Staff, "I assume you ladies and gentlemen have all seen E.T....They're nowhere near that nice." The series was produced by Steven Spielberg, the director of E.T., and may also reference the aborted E.T. sequel, E.T. II: Nocturnal Fears, that was to feature evil albino E.T.s that abducted people.
In "Charlie and Lisa" and "God's Equation", Lisa Clarke has a poster for the 1958 film I Married a Monster from Outer Space in her apartment. This is a reference to the fact that Lisa's grandmother Sally had a relationship with the alien John in "Beyond the Sky".
In "God's Equation", Ray Morrison demands that Dr. Harriet Penzler call the FBI and put her through to whoever runs the extraterrestrial project. Cynthia sarcastically asks, "You wantWill Smith or Tommy Lee Jones?" When Ray later asks the same thing of Mary, she says, "Like on X-Files?"
Also in "God's Equation", Cynthia contemptuously says that she has been "abducted by Homer Simpson" after Ray takes the therapy group hostage.