When Booth and Brennan enter the UFO diner, Booth sees a framed photo and says, "Oh, Rocketship 7!" The man in the photo is Dave Roberts "Dave Thomas," the host of the morning children's program "Rocketship 7," which ran on WKBW-Buffalo from 1962-78 and also David Boreanaz 's (Booth's) father.
Dean Haglund who played Blaine Miller in this episode played Richard Langly in both The X-Files (1993) and its short lived spin off The Lone Gunmen (2001)
The title is a play on the series "The X-Files" which also aired in Fox from 1993 - 2002 that investigated paranormal activity. When cell phone rings in the desert, it plays the theme song from the show.
Three of the guest stars in this episode also appeared on The X-Files (1993) : Dale Dickey , as shotgun lady Marsha Vinton; Penny Johnson Jerald, as business executive Rachel Adams [the actress also played Captain Kasidy Yates on another great sci-fi series, Star Trek: Deep Space Nine (1993) ]; and, of course Dean Haglund, as cafe owner, Blaine Miller, who was an X Files regular, as Richard 'Ringo' Langly, one of that wonderful trio of conspiracy investigators, The Lone Gunmen, who also had their own, far too short series, The Lone Gunmen (2001) .
In Aliens in a Spaceship (2006), the team is called to investigate an object thought to be a spaceship with aliens inside. This is of course nonsense and introduced the Gravedigger serial killer, who had buried two young boys alive in a large vat. When Brennan declares it to be such, Booth says the line, "I liked it better when they were aliens." This line is said again, by Angela, when it is discovered again not to be aliens and is instead a suspect dumping chemicals illegally in the desert.