In a conversation about Melissa Turner being suspected of witchcraft with the Chief, Scully mentions that it wouldn't be the first time such false accusations had been made in local parts. This is a reference to the fact that Maine was a part of Massachusetts when the Salem Witch Trials were going on.
When Scully mentions the possibility of a possessed doll being involved in the killings, Mulder jokingly mentions the famous horror character Chucky. Brad Dourif, who provides Chucky's voice in the films, appeared in the thirteenth episode of Season One as the psychic convict Luther Lee Boggs.
Original name of this episode was Chinga - but it was rejected by Fox as it may have been an objectionable word in some Spanish speaking areas. The name 'Bunghoney' was substituted - a rude sounding but nonsensical term. Chinga was later brought back, it means f*ck (or a similar, general expression of disappointment).
The movie milder is watching is called "Alien Probe" though he says it's "deadliest swarms" and the noises indicates it is pornographic, a trait of his character. The title of the film is on the open clamshell on his desk.