Fiery Coverup: The Cigarette Smoking Man orders soldiers to burn down a boxcar with hybrid alien bodies. Mulder was inside of said boxcar as well. Probably. Or not.
Hollywood Hacking: Somewhat averted in that the hacker is seen waiting for his program to do the actual hacking, seemingly having been there a while, as opposed to the instant access typing usually seen on TV.
Percussive Prevention: Sometimes characters help their friends by punching them unconscious. Scully takes it Up to Eleven when she shoots Mulder to prevent him from killing Krycek.
Percussive Therapy: Mulder, enraged that he got yet another fake instead of top secret information, smashes a pencil holder against the wall in his office. The files were actually encrypted, not gibberish.
Unfamiliar Ceiling: Twice. First when confused Mulder wakes up at Scully's and then at Albert Hosteen's in New Mexico.
Water Source Tampering: The Syndicate puts LSD or similar drug into Mulder's water supply, causing erratic behaviour that discredits both him and the case he is currently following. And since it wasn't just Mulder's water supply, but his entire apartment building's, it also caused at least one murder there.
You Killed My Father: Krycek kills Mulder's father and tries to frame Mulder. Scully averts the actual revenge because if she hadn't stopped Mulder from killing Krycek, Mulder would have been found guilty.