The Post-Modern Prometheus - S5-E5
[After spilling coffee on his lap.]
Mulder: Great, now my crotch will be up all night.
Deep Throat - S1-E2
Mulder: They're here, aren't they?
Deep Throat: Mr Mulder, they've been here for a long, long time. (00:49:58)
Clyde Bruckman's Final Repose - S3-E4
Clyde Bruckman: You know, there are worse ways to go, but I can't think of a more undignified way than autoerotic asphyxiation.
Mulder: Why are you telling me that?
Clyde Bruckman: Look, forget I mentioned it. It's none of my business.
Answer: As he stated many times throughout the series, Mulder needed Scully to be sober and skeptical. Whenever Scully's skepticism wavered and she started questioning her own rationality, Mulder would try to restore her sense of skepticism, because he needed her to be clear-thinking.
Charles Austin Miller