No way is Scully an INTJ. She may be a scientist by profession, but (speaking as an INTJ myself) she would never take seven years to admit to "kind of" believing in the paranormal if she were an INTJ. No, I agree with most people on this board. She's definitely an ISTJ. She's committed to traditional values. She's extremely responsible. She's very judicious and organized. That's why Mulder pisses her off so much sometimes.
As for Mulder, he's an INFJ, usually. For a while, I thought he was an INFP, but he's not that self-loathing. Most people would agree that Mulder's an INXX. As for the F, I think that's rather obvious. Chris Carter and others have admitted that they created Mulder and Scully to be kind of the opposites of society's assumed gender roles. Mulder is emotional (at least to a degree), while Scully is logical. I mean, Mulder graduated in psychology and was a brilliant profiler at the FBI for a while. He's an F who can also be quite logical, but he's clearly an F. He reacts with much more emotion than Scully in the series, whether with anger, frustration, or guilt.
Anyway, INFJ really fits. INFJs dominant attribute is their intuition. Mulder is nicknamed "Spooky" for his wild, but uncannily accurate theories. He can read people very easily. INFJs aren't good with the little details, like paperwork, which is why Mulder needs Scully to help him legitimize his work all the time. INFJs also love working independently and stick to their ideals fiercely. That's definitely Mulder.
Of course, he has some P tendencies at times, but I think he is maybe about 5% more J. He knows where he's going and what he believes, and he usually isn't dissuaded from that. In the series, Mulder and Scully often have an "agree to disagree" attitude about their partnership. Mulder believes he's always right, and so does Scully. That's the whole dynamic of the show: two fairly decisive people who mostly stick to their guns about their beliefs (although I think Scully is often simply in denial...classic).