During the opening scene (post credits), the camera pans past several gravestones. The name on one of the gravestones is Raymond Soames. Ray Soames is a character in Pilot (1993) about whom the plot revolves.
Scully awakens in bed by a phone call from Mulder at 11:21pm, just like in season 1 pilot and finale.
Agent Bocks' mention of "that kid from Wisconsin" is likely a reference to serial killer Jeffrey Dahmer.