The Forest for the Trees
There are "woods" on two different levels in In the Woods. On the physical level, you can't miss them. The woods around Knocknaree are where Rob's friends disappeared in the eighties and where young Katy is found murdered in present-day. Some people believe there are monsters in the woods, and these beliefs are so strong that sometimes people see strange shapes or hear creepy noises, although no hard evidence of any strange supernatural beast actually prowling the woods is ever definitively found.
The woods are being threatened by the impending highway project, so the archeologists are working as fast as they can to see what is preserved in the ground before it's obliterated by a ribbon of asphalt. They are working against time, just like the detectives. And while most of their findings are standard fare—think: arrowheads—they also discover the corpse of a child displayed on a sacrificial alter.
The woods referred to in the title, then, on one level are a shout-out to everything that happens in the Knocknaree forest, from the terror in the eighties to Katy's murder to the archeological world to the impending highway.
Rob's memories are like woods, too, though. He says, "In ways too dark and crucial to be called metaphorical, I never left that wood" (2.99). As he tries to rebuild his memories from the time his friends went missing, it's just like the archeologists searching the woods. Instead of trying to search the woods before they build a highway, though (no one is going to build a road through Rob's head), he has to search fast to solve a present-day murder that might be linked to a decades-old cold case.
Just as the woods have been shrinking in real life thanks to some trees being cut down over the years, his memories feel smaller to Rob now that he is older. He says, "The strip of trees was what was left of it" (2.24)—in other words, he's forgotten so much that he has no clue what's going to turn up. Some of it is dark and mysterious and he doesn't know what to make of it, just like the mysterious beast that may or may not be prowling the woods. And sometimes he remembers something that he wishes he hadn't, like witnessing a gang rape in the clearing.
So the moral of this story is, whenever you go in the woods, whether in real life or your wooded memory, pack a flashlight. It's dark in there.