RonnieStein drops The Flash back on the ground at the base of a bridge in episode 1x13 "The Nuclear Man".
H.R. writes a fictionalized version of the team's busting of a gun sale with himself as the hero in episode 3x11 "Dead or Alive".
Clive and Liv investigate the boat where the murders occurred in episode 2x12 "Physician, Heal Thy Selfie".
Deep Throat calls Mulder to talk about the Litchfield program in episode 1x11 "Eve".