A novel by Joseph Conrad. Heart of Darkness and its influence appears a few times in Season 3. One of the most salient aspects of the novel is the narrative frame in which it was told. Stiles apparently retains this information, because he uses it when listening to Peter talk about Derek in 3x08 - Visionary. He understands that a story transforms as it moves from one narrator to another, so the story of Paige, when told by Derek, might be a quite different one.
The title becomes a phrase that Dr. Deaton uses to describe what will happen to Scott, Stiles, and Allison if they sacrifice themselves to the nemeton in place of their parents. They will have "a darkness around their hearts."
Heart of Darkness was a study on the nature of evil, a theme carried very strongly through Season 3. Who is evil? What makes them so?
Jennifer Blake is evil by the accounts of the people she has murdered. However, she claims her actions were to defeat an even greater foe. She characterizes her actions as bad but necessary, therefore not evil.
Deucalion wasn't always the man he became. He used to be peaceful and reasonable, but wrongs done to him twisted him into someone who seeks power and vengeance. So evil is contractible? Like a disease? Something he caught from Gerard Argent on the day he was blinded. Like Kurtz in the novel, Deucalion becomes consumed by his greed, only he lusts after power instead of money. His darkness corrupts other, turning once good werewolves into traitors and murderers who fall for the greed of the path he has chosen. The ivory traders in the book traded their morals for profit; Deucalion makes a similar trade.
Take also Peter's manipulation of Derek into causing Paige's death. Were there ulterior motives to his manipulations that render his actions anything other than pure evil? And Derek killing Paige to end her suffering: where does this fall on the scale of right and wrong?
Heart of Darkness provides no answers to these questions, but the allusion opens up questions about the story being told in 3A in terms of stories as tales told by individuals and not records of truth and evil as a concept that lives, or doesn't, in the human heart.