In Independence Day, one man thinks that an alien invasion is a joke and says that yeah, he likes The X-Files too.
Live Action TV
Castle did a whole episode to homage The X-Files. Castle whistles the theme song, Becket is called Scully, they become entangled in government project, and the villain is called the cigarette smoking man.
Bones: When Bones and Booth investigate a weird case, the theme songs starts playing... Too-doo-dooo-DOOO-dooo... Turns out it's the victims mobile phone.