An Arm and a Leg: Mulder loses his arms, and is promised that they will cut off his legs as well unless he cooperates. Luckily, it was just virtual reality.
Creepy Blue Eyes: The doctor has Creepy Blues, enlarged by his huge glasses. Oh God, the look he gives to Mulder when he's about to amputate his arm...
Dressed to Heal: The nurses and the doctor who rush Agent Mulder into an operating theatre look a little too much nurse-like and doctor-like in their obsolete white outfits. Especially the nurses' caps. It's the first but very subtle hint that Mulder is trapped in a virtual reality simulator.
A Glitch in the Matrix: Mulder realizes that his reality is not real when Scully saves him from evil nurses, but is not compassionate and comforting about his amputated limbs. The reality from his perspective starts to short out.
Lotus-Eater Machine: Mulder in the hospital scene is less of a utopia than is usual for this trope, but the sexy nurses might be a product of his imagination induced by his porn habits. Ass-kicking Scully who comes to his rescue is not unlike her real self, but it's undoubtedly enhanced.
Ominous Visual Glitch: Mulder is trapped in a virtual reality simulator. When he realizes that it's not real, the reality from his perspective starts to short out. He sees the glitches and fake Scully dissolves into an image of animated person.
Soundtrack Dissonance: Romantic "Twilight Time" by the Platters plays when a building is blown up and later when a woman has her consciousness sucked out.
Why Don't You Just Shoot Him?: Mulder asks why the AI didn't use the Kill Sat on his creator. Apparently it was done as a sign of respect, the computer having to come up with something suitably clever.