Wayne walking up the spiraling staircase in the dark holding a glowing glass of milk (which the audience knows has been "spiked" with a substance) is an homage to the classic Cary Grant scene.
Mulder refers to the kids as Speed Racers
Scully mentions Rosemary's Baby (1968)
episode title reference
Playing on the television as Mulder and Scully walk through Wayne and Betsy's house