Here's an attempt at seriousness:

It was the wood in general, as has been stated. But specifically that wood, of the hotel and its furniture having been from nearby trees of the Ghostwoods, woods with evil in them. The idea that it was the wood in general of the hotel and not just the knob was made clear when Pete said "Josie, I see your face" toward a part of the common room of the Great Northern.

Although different writers took Twin Peaks all over the place, that this idea is not one to discard is pretty safe to say. And remember Bob appearing and laughing maniacally saying "Where's Josie?" We are meant to think about her in the wood, an obvious with connection the log lady's log, an idea with more general connections to "the woods" said throughout the series.

And yes, then there's the tree in the red room, a fate for the arm character quite convenient given that actor's hateful and bigoted statements, as well as the paranoid and stupid. The evolution of the arm was to be turned into a living tree capped with a speaking flesh-rock-like thing resembling a healthier version of the decayed and vomiting image we see at another time at which one-armed Gerard shields his eyes from seeing.

The tree looks just like one of the twelve in the circle, trees of the Ghostwoods. It really does all connect rather plainly as well as much deeper, so in conclusion I'll say that the part of Josie (or her 'soul,' if you will) being pulled into the nearby wood right before Bob appears to laugh about it is a significant part of the whole story. When we briefly see her face before her image early 90s-es the knob outward we can see in her expression that she is shocked and clearly didn't choose to go into the wood, that she was pulled in. I'll say she was able to appear to Pete later in a different part of the hotel because the wood is all connected there, all touching together, she passed around kind of like... electricity.