In the scene where Mulder detects the scent of his favorite perfume, there are only five people in the police station.
SCENE 14 (At the precinct) WHITE: Let me get this straight, for the
record; you haven’t seen the bag in a year and you sold it at a garage
GODFREY: To a young girl, one of the Roberts family. They live a few
WHITE: Why was it filled with bones and buried in the middle of a
GODFREY: I have no idea.
WHITE: Well, the people of this town seem to think you do. Would you
be willing to take a lie detector test?
SCULLY: You can go now Dr. Godfrey, I don’t think we’ll be needing you
any further. Your story checked out.
GODFREY: Thank God. (Gets up and puts on jack, standing behind
SCULLY: The bones, turned out to be the skeletal remains not of an
infant, but of a beloved, fourteen year old [lasa apso], formerly
known as (holds out collar) Mr. Tippy.
(Terri enters the room.)
TERRI: Mr. Tippy…
MULDER: This may not be any time to mention it, but someone is wearing
my favorite perfume.
We have Mulder, Detective White, Godfrey, Scully, and Terri.
Mulder obviously is not wearing the perfume himself. He determines that it is not Scully.
MULDER: (Loses interest, starts sniffling the air, closing in around
SCULLY: I see no reason to pursue this case any further and not only
that, I find your conduct and comportment in this investigation not
just alarming, but highly objectionable. What are you doing?!
MULDER: (slightly distracted.) Must be detective White…
He tries to determine whether Detective White is wearing the perfume:
WHITE: (upset) If they’re not Satanists, who are they?
(Mulder walks to her and embraces her comfortingly, then starts
sniffling her perfume.)
WHITE: (pushing him away.) What are you doing?
Although there is no indication in the script that Mulder determines that Detective White was not wearing the perfume, the impression I got from the scene was that she was not. However, it is possible that Detective White was the one wearing the perfume.
The other possibilities are Terri and Godfrey. As mentioned in the comments by @Dan Bron, Godfrey, who engages in occasional cross-dressing, is implied by the camera work to be the one who is wearing the perfume. That said, we cannot definitely rule out the possibility that Terri is the one wearing it, or indeed that Detective White wasn't wearing it.