The Subtle Knife
The titular Subtle Knife is a symbol in this novel for nuance and discernment. By discernment, what is meant is telling one thing apart from a very similar thing. That act requires subtlety and precision, and since there are forces that are trying to control Lyra and her friends, they have to be covert and clever. They are in a dilemma where only scrutiny can help.
The Alethiometer
There is a fictitious instrument used by Lyra in her attempts to become more knowledgeable in the truth. She uses this meter, literally Greek for "truth meter," and that's exactly the service it provides. In situations where their emotions aren't clear, and when other people are pressuring their decisions, the gang relies on Lyra's grasp of truth to figure out what to do.
Lyra's disappearance
Lyra is lost by the group, leaving Will at the end of the novel alone to find her on his own, but he doesn't even know if she's alive. All he has is her trusty tool, the Alethiometer, and the difficult challenge of learning from her example, literally to honor her. Her disappearance from the end of the novel is a symbolic representation that her friends are having to learn from her heroic example.
The witch
There is something archetypal about the arch-villain of this story, the witch who wants Lyra for her own occult purposes, purposes that are rooted completely in superstition and religious belief. She represents two things at least: the divine feminine nature of human death (which we're "running away from") and the grips of superstitious belief (symbolized by her being a literal witch).
The motif of darkness
In obscurity, there are unknowns. There are the "shadows" of this novel, which paint a solid picture of when there are threats lurking in the darkness, and so the darkness represents something typical and mythic: threat assessment. The use of negative vibes in this novel is a way of showing that the characters are in the "threat assessment" business. They are discerning when they are safe and when they are not. Chronic emotional damage weakens this ability, so they fight against bias.
