Redux

Mulder: "If I did indeed have the cure for Scully's cancer I
         was now as dependent on her as she was on me. As I had
         breached this facility, I needed to find my way out to       safety, depending on Scully to weave her story, to tell her tale, 
to make them believe the lie."

Mulder: "Did they give Agent Scully this disease? Did they
         do this because of me?" 

Scully: "Mulder, how long has this been going on?" 
Mulder: "Maybe since the beginning, since you joined me on
         the X-Files." 
Scully: "That would mean that for four years we've been
         nothing more than pawns in a game. That it was a lie from the
         beginning. Mulder, these men, you give them your faith and
         you're supposed to trust them with your life." 
Mulder: "There are those who can be trusted. What I need
         to know is who among them is not. I will not allow this
         treason to prosper, not if they've done this to you." 
Scully: "Mulder, we can't go to the bureau making these
         accusations." 
Mulder: "No, but as they lie to us we can lie to them. A lie to
         find the truth." 

Redux II

Bill Scully: "Has it been worth it? To you, I mean. You found
              what you've been looking for?" 
Mulder: "No." 
Bill Scully: "No. You know how that makes me feel?" 
Mulder: "In a way I think I do. I lost someone very close to
         me. I lost a sister, I lost my father. All becuase of this thing
         I'm looking for." 
Bill Scully: "It's what? Little green aliens?" 
Mulder: "Yeah. Little green aliens." 
Bill Scully: "You're one sorry son of a bitch." 

Mulder: "One sorry son of a bitch speaking."

Skinner: "Scully will verify all that." 
Mulder: "That's a good place to lay it, considering her
         condition." 
Skinner: "Do you want me to lay it where it belongs, Agent
          Mulder?"

Detour

Scully: "I must remind you that this goes against the Bureau's
         policy of male and female agents consorting in the same motel
         room while on assignment."

Scully: "What do you think killed those men?" 
Jeff Glaser: "Nature is populated by creatures either trying to
              kill something they need to survive or trying to avoid being
              killed by something that needs them to survive. If we become
              blinded by the beauty of nature, we may fail to see its cruelty
              and violence." 
Scully: "Walt Whitman?" 
Jeff Glaser: "No. 'When Animals Attack' on the FOX network." 

Mulder: "Who cut the cheese?"

Scully: "Where are you going?" 
Mulder: "I'm gonna check something out." 
Scully: "You know, Mulder, sometimes I think some work on
         your communication skills wouldn't be such a bad idea." 
Mulder: "I'll be back soon and we can build a tower of
         furniture, OK?"

Scully: "Ever thought seriously about dying?" 
Mulder: "Yeah, once, when I was at the ice capades."

Mulder: "Kill me now."

Mulder: "I know these things." 

Mulder: "How do I say this without using any negative words, Scully?"
Scully: "You want me to tell them that you're not going to
         make it to this year's teamwork seminar." 
Mulder: "Yeah. You see that? We don't need that
         conference. We have communication, like that, unspoken,
         you know what I'm thinking."

Mulder: "...Witnesses described them as primitive-looking
         men with red, piercing eyes. Became known as the
         'mothmen.' I got an X-File dating back to 1952 on it." 
Scully: "What would that be filed next to, the Cockroach That
         Ate Cincinnati?" 
Mulder: "No, the Cockroach That Ate Cincinnati is in the
         'C's; Mothmen's over in the 'M's."

Mulder: "Par-tay!"

Mulder: "You know, I hear that the best way to regenerate body 
         heat is to crawl naked into a sleeping bag with someone 
         else who's already naked." 
Scully: "Well, if it starts raining sleeping bags, you might get
         lucky." 

Mulder: "Try any of that tailhook crap on me, Scully, I'll kick
         your ass." 

Mulder: "I don't wanna wrestle."

PMP

Mulder: "Scully, do you think it's too soon for me to get my 
         own 1-900 number?"

Scully: "Peanut butter sandwiches?" 
Mulder: "You think bologne would be more effective?"

Mulder: "I'm alarmed that you would reduce these people to a 
         stereotype.  Not everybody dreams to get on Jerry Springer."

Scully: "Is there anything that you *don't* believe in, Mulder?"

Scully: "Sir, unles you want your scientific achievements to 
         end up as a footnote on the Jerry Springer Show, I 
         suggest that you make the time."
Mad Doc: "Jerry Springer show?"

Mulder: "The other victims... they had their frying pans... violated."

Scully: "Mulder?" 
Mulder: "You may have been right, Scully." 
Scully: "What, that these people could be reduced to a cultural stereotype?"

Mulder: "This is all wrong, Scully.  This is not how the story's 
         supposed to end." 
Scully: "What do you mean?"
Mulder: "Dr. Frankenstein pays for his evil ambitions, yes.  But the 
         monster is supposed to escape, to go search for his bride."
Scully: "There's not going to be any bride, Mulder.  Not in this story." 
Mulder: "Well, where's the writer? I want to speak to the writer." 

Kitsuegari

Marshall: "So what's adequate backup?" 
Mulder: "Adequate backup? Every cop you can lay your hands on."

Scully: "That's one hell of a plan, Mulder. A serial killer makes us 
         believe that he's guilty in turn diverting the suspicion away
         from the real estate lady?  Well, he had me going!"