In Independence Day, one man thinks that an alien invasion is a joke and says that yeah, he likes The X-Files too.
In Odd Thomas, Odd's girlfriend Stormy calls him Mulder when she thinks he's being overprotective. He only calls her Scully if he's willing to get smacked for it.
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 a 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.