I've always really, really loved this moment, ever since I watched it live in 1998. It's small, and maybe it's silly, but there's something endearing about the Scullycentrism of it. This episode is extremely Mulder-focused—in both the 1933 timeline, which is in Mulder's POV, and the 1998 timeline, which is in Scully's POV but is completely about Mulder—and the question that hangs over the episode (at least for me) is about their bond; a kind of "Will she recognize him?" (Not literally, but in a spiritual sense.) And ultimately, we get the answer to that question: "Yes, she will. Not completely, but enough to believe him and do as he asks, thus saving him and herself and the whole world."
But this moment is A Scully Moment. She senses something at that spot in the hallway, and she doesn't know what it is, but she feels that recognition that we've been yearning for. "I know you. You're dear to me." And for My Girl to have that overt, absolute recognition not for Her Man but rather for herself is... I don't know. There's something healing, and beautiful, and proud, and self-loving about it.