Season 2's "Anasazi" and Agent Skinner's setting of a new world record in Badass. After a whole season of being the Cigarette-Smoking Man's Chew Toy and helplessly watching the attempted murders of both Mulder and Scully, he finally gains the upper hand:
(Skinner summons an elderly Native American man into the room where CSM is confronting him) CSM: What is this? Skinner: This is where you pucker up and kiss my ass. CSM: Now, listen you— Skinner: Now you listen to me, you son of a bitch! This man's name is Albert Hosteen. You should remember that. Because if Agents Mulder and Scully come down with so much as a case of the flu, Albert is prepared to recite, chapter and verse, file for file, everything on your precious tape. CSM: It's a nice try, Skinner. Skinner: I'm sure you're thinking Albert is an old man and there are plenty of ways you might kill him too. Which is why, in the ancient oral tradition of his people, he's told twenty other men the information on those files. So unless you kill every Navajo living in four states... that information is available with a simple phone call. (smirks) Welcome to the wonderful world of high technology. (CSM stares in disbelief) CSM: You're bluffing. Skinner: Am I?
Similarly, Skinner got one CMOA for reopening the X-Files in "Ascension", specifically because "It's what they fear the most."
That whole episode is a case of From Bad to Worse for CSM in general, since most of his assurances to his fellow Syndicate members are proven to be lies. He first failed to kill Mulder, then failed to catch Mulder and Scully, and lost the DAT tape — to Krycek who he also failed to kill. His expression when he hears Krycek on the phone is priceless, especially since he's trying not to let the other members know what he's actually hearing. Since he's normally such a Magnificent Bastard, watching him screw up is a CMOA on its own.
This is later revealed to be true because he assassinated JFK.Or not.
The episode "Unusual Suspects" looks at the formation of the Lone Gunmen, Mulder's geeky online allies. Throughout the episode, the "subversive" Frohike and Langley look down on Byers, a government employee, frequently dismissing him with the sneer that he's a "Narc". Yet at the end, when they're surrounded by conspiracy agents who could kill them at any moment and have had the truth of the plot revealed to them, it's the "Narc" who gets up on his feet and angrily demands who the hell gave these guys the right to act like they can do whatever the hell they want, facing the fact that these guys could shoot him instantly without even flinching, whilst Langly and Frohike are desperately trying to get him to shut up.
"Paper Hearts": Mulder sinks the basket.
Monica Reyes calling out the prosecuter in "The Truth".
Kallenbrunner: She gave up the miracle child? The proof of everything that she and Mulder claim they have risked their lives for over the last nine years? She just sent it off to some strangers? Monica: Yes, to protect him! Kallenbrunner: Thank you, Agent Reyes. That is all. Monica: You don't care about that child or what Scully had to sacrifice. You are only too happy she had to give it up so there's no proof. Kersh: Agent Reyes. Monica: You don't care what these people have sacrificed over the last nine years—what's been lost to their cause. You make a mockery of it, gladdened that it proves your point. Kersh: Agent Reyes, that's enough! Monica: What's the point of all of this? To destroy a man who seeks the truth or destroy the truth so no man can seek it? Either way, you lose.
Skinner and Doggett breaking Mulder out of prison in "The Truth".
Mulder rescuing Scully from an alien spaceship in Antarctica in The Movie.
Also Scully giving her reason why they should continue working on the X-Files as long as they are allowed. It implies that they are looking for the truth so that they can help people and save the planet, no less.
Scully: I can't [quit the FBI and be a doctor]. I won't. Mulder, I'll be a doctor, but my work is here with you now. That virus that I was exposed to, whatever it is, it has a cure. You held it in your hand. How many other lives can we save? Look, if I quit now, they win.
Scully returning from Cote d'Ivoire and kicking every ass in sight until she got Mulder back in "The Sixth Extinction: Amor Fati".
Apart from everything Scully does to save Mulder, she also bitches him out in his drugged state because he had given up the fight. Read: even in his subconscious, Scully is his constant, his touchstone.
Scully in "Beyond the Sea" to "psychic" Luther Lee Boggs:
Scully: You set us up. You're in on this with Lucas Henry. This was a trap for Mulder because he helped put you away. Well, I came here to tell you that if he dies because of what you've done, four days from now, no one will be able to stop me from being the one that will throw the switch and gas you out of this life for good, you son of a bitch!
Note that she's actually incorrect in this accusation.
Earlier, Mulder presents Boggs with several pieces of evidence to test his claims of mental powers. After Boggs goes through a whole routine on a piece of a shirt, Mulder reveals that it has nothing to do with the case, and he just cut it off one of his own shirts.
The episode "Triangle". The first three acts are entirely The Oner, and the last one builds to a stunning climax with a Suspiciously Similar Song to "Sing Sing Sing." Plus, the incredible split screen shot where the two Scullys switch places.
Basketball fans will like this one. In "Musings of a Cigarette Smoking Man" CSM mentions he drugged the Russian goalie in the Olympic hockey finals against USA, in response to the infamous basketball game where the final three seconds were replayed three times so the Soviets would win.
CSM: Payback's a bitch, Ivan.
For that matter, Cancerman looking out the window after Mulder dies, watching the aliens invade.
Mulder breaking the fourth wall in "The Post-modern Prometheus", all to petition the writers for a happier ending. However, all depends on your interpretation of this post-modernistic piece of a story. You might think that he wasn't petitioning the writers of the show, but the writer of the comic book, the boy whose mother was the one to phone in the case to the FBI. Your view may vary on the fact whether the concert and the dance did really happen - in the comics it did certainly, but did it happen in-universe in Mulder and Scully's reality?
In season 8 finale, Walter Skinner finally kills Alex Krycek with a well-placed and well-deserved headshot.