Since the start of the first season of The X-Files, every episode has had a cryptic phrase shown at the beginning, during the introductory credits. For almost all the episodes, this quotation is "The Truth Is Out There". Several times during the history of The X-Files, though, this has been replaced with other phrases.
1. 
Standard phrase throughout The X-Files, and Mulder's favourite saying. Appears in almost all episodes.
2. 
Deep Throat's last words to Scully as he lay dying from a gunshot at point-blank range. Appeared in the episode "The Erlenmeyer Flask".
3. 
Mr. X summed up the government's policy on what happened to Agent Scully. Appeared in the episode "Ascension".
4. 
This is the Navajo translation of "The Truth Is Out There". Appeared in the episode "Anasazi".
5. 
The Alien Bounty Hunter told Mulder that "everything dies", but Marita Covarrubias told Mulder at the end of the episode that "not everything dies." Appeared in the episode "Herrenvolk".
6. 
This was a phrase that was mentioned by Scully and was heard a few other times through the episode "Teliko". Appeared in the episode "Teliko".
7. 
Galileo mumbled this while he was forced to stand before the Inquisition to state that the Earth didn't rotate but that the Sun went around the Earth. It means "But it does move." Appeared in the episode "Terma".
8. 
This is what Scully said in front of the FBI panel of officials in the episode. She was referring to Mulder being led to believe in the biggest of lies, the existence of aliens. Appeared in the episode "Gethsemane".
9. "All Lies Lead To The Truth"
This is what Scully mused during the episode, in referring to how the lie Mulder and her had perpetrated to the conspirators would expose the real truth. Appeared in the episode "Redux".
10. "Resist or Serve"
This is in reference to what the humans would have to decide to do if the warring aliens decided to colonize Earth. Appeared in the episode "The Red and the Black".
11. "The End"
This was the actual title of the episode it appeared in, which is a first in the X-Files. It refers to how the actual X-Files office was destroyed in a fire set by the Cigarette-Smoking Man, and how the Justice Department wanted to reassign Scully and Mulder to separate departments to effectively end The X-Files division. Appeared in the episode "The End".
12. "Die Wahrheit Ist Irgendwo Da Drauben"
This is apparently "The Truth is Out There" in a German dialect. Appeared in the episode "Triangle".
13. "The End"
This tagline, originally from the episode "The End", was repeated here, although in a different context. In this episode, it meant death (the final ending) in general, or in Felig's final ending after his extremely long life. Appeared in the episode "Tithonus".
14. "In The Big Inning"
This episode was about an alien who loved baseball. Appeared in the episode "The Unnatural".
15. "Amor Fati"
In this episode, Cigarette-Smoking Man announces to Mulder that "I'm your father." Appeared in the episode "The Sixth Extinction II".
16. "Believe to Understand"
This refers to Mulder having to believe Piller's visions in order to understand what happened to his sister. Appeared in the episode "Closure".
