When Scully is reading her e-mail from Mulder, her user ID is "queequeg0925." "Queequeg" is in reference to Scully's favorite novel, "Moby Dick," as well as her dog in Season 3. "0925" is in reference to the birth date (September 25th) of Gillian Anderson's daughter, Piper.
Terry O'Quinn (Shadow Man) previously appeared in Aubrey (1995) as Lt. Brian Tillman and The X Files (1998) as Agent Darius Michaud. He also played Peter Watts in the companion series Millennium (1996). In this one, he is atypically credited as Terrance Quinn rather than his usual performing name.
In the scene of the bench, clearly visible is the tattoo that Gillian Anderson has on her right wrist.
The email addresses that Mulder and Scully use were real ones, maintained by 1013 Productions.
Technically this is the first appearance of Mulder in the season but only through archive footage, a method that would only be repeated twice in Jump the Shark (2002) and William (2002).