Scully: You'll be in my prayers
Mulder: Have your father say a few Hail Mulders for me.
Mulder: Live the lie, you have to believe it. Like these men who deceive us, who gave you this disease. We all have our faith. And mine is in the truth.
Scully: Mulder, if I can save you, let me.
Skinner: You look pretty good for a dead man.
Mulder: I'm only half-dead.
Scully: So why'd you come here if you already made up your mind?
Mulder: Because I knew you'd talk me out of it if I was making a mistake.
Mulder: Please tell me you're here with severe chest pains.
CSM: You should be glad for why I'm here, pay you some respect.
Mulder: Go to hell.
CSM: For your cleverness, and your resource, what you managed to do for Scully.
Mulder: What are you talking about?
CSM: Well, breaching the security at the Defense Department Facility. Finding the cure for her disease.
Mulder: What I found was useless.
CSM: On the contrary, it's essential to her survival. If you like, we could step outside and I might explain myself? I'm here tonight as a friend, Agent Mulder.
Mulder: You murdered my father, you killed Scully's sister, and if Scully dies, I will kill you. I don't care whose father you are, I will put you down.
Mulder's threat to CSM, "I don't care whose father you are, I will put you down", is a poignant piece of foreshadowing as we are introduced to Agent Jeffrey Spender later this season in 'Patient X', who we learn is CSM's son. It may also be significant in that many believe that CSM is Mulder's real father.
In response to the above, I actually think that this is a reference to Samantha's claims that CSM is her father, and to Mulder's previous questioning of his mother's relationship with CSM - in other words, Mulder believes CSM is the father of his sister.