i think Deep Throat doesn't reappear in the Truth because he has already been in Mulder's mind in The Sixth Extinction. in addition, Deep Throat admits that he has happy life, gets married and has kids. so we've got Krycek, Mr. X and Line Gunmen in The Truth, not to mention a very alive CSM.
btw, have you all known that actually in the original script Scully had a boyfriend in Pilot? fortunately CC knew that Scully's scenes w/ a boyfriend wouldn't do any good to the plot. so he decided to keep the boyfriend in the deleted-scene parts only. thank God!
one thing i noticed in Season 1 is Scully's hair, big flashlights and out-of-dated cellphones
