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.
This is later revealed to be true because he assassinated JFK.Or not.
The episode "End Game" had badasses Skinner and X kicking each others asses in an elevator to find Mulder.
In "Anasazi", an unarmed Mulder manages to take down an armed Krycek by sneaking up on him and wrestling him. It was only Scully's intervention that saved Krycek.
Then he does it to Krycek again in "Piper Maru".
"Paper Clip" 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?
We later learn that not only was he bluffing, but Mr. Hosteen had no clue why Skinner invited him into the office until the speech.
Similarly, Skinner got one CMOA for reopening the X-Files in "Ascension", specifically because "It's what they fear the most."
Watching the Cigarette Smoking Man get called by Skinner in "Paper Clip" and him panicking about the tape is Awesome in it's own right.
To Recap that episode Krycek had been exposed as a mole who murdered Duane Barry and the skylift operator and had sold Scully leading to this exchange.
Skinner: Let it go Mulder there's nothing you can do
Mulder: What can YOU do about it?
Skinner: There's only one thing I CAN do Agent Mulder. As of right now I'm reopening the X-Files. That'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.
From "Clyde Bruckman's Final Repose":
Scully: All right. How do I die? Clyde Bruckman: You don't.
And in a later episode Scully actually does appear to become immortal.
Also from this episode: Scully lets the sexist detective blather on about how he dislikes women being part of his investigation. She proves him wrong by her top-notch professional performance.
In "731", MrX arriving just in the nick of time to gun down the Syndicate assassin who nearly murdered Mulder, then carry the injured agent to safety just before the train explodes. The kicker? Mulder never finds out that it was Mr X who saved him.
"Piper Maru": Scully identifying an airplane's model from wreckage at the bottom of the ocean. Mulder replies "I just got very turned on."
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.
"Paper Hearts": Mulder is dared to sink a half-court shot. He proceeds to casually do it in one shot. Doubles as a meta Moment of Awesome, as David Duchovny sunk the basket in one take, no special effects.
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.
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 "Mind's Eye", Mulder, Scully and a detective are interrogating a murder suspect, who keeps dodging their questions while taunting and mocking them. Mulder decides to play her game, and with just a few choices words cuts through her like a knife, leaving her speechless and making her lose her cool.
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.
Scully returning from Côté 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.
In "Orison," serial killer Donnie Pfaster lets a call girl into his apartment and, in accordance with his MO, asks her to take a bath and wash her hair. The viewer is set up to expect an example of Disposable Sex Worker but when Pfaster tries to get violent, she throws hot wax in his face, punches his lights out and leaves. It's especially pleasurable to watch because Pfaster hates women and has tended to kill sex workers, so this is a kind of vicarious revenge.
In season finale, Walter Skinner finally kills Alex Krycek with a well-placed and well-deserved headshot.
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".
In the second episode of the revival "Founder's Mutation," when Kyle and Molly use their Twin Telepathy to kill Goldman and escape from the hospital Molly had been kept prisoner in.
Scully's incredibly nonchalant takedown of a suspect in "Home Again": she puts down an armed suspect in about three seconds flat while wearing stiletto heels, then casually hands the suspect's gun to a shocked Mulder.