This Official Walkthrough Chart guides you through all the puzzles in all three acts of the game. It's also the actual chart that I have been using to keep track of puzzles, the triggering of cutscenes and whatnot during the actual development of the game. I think of it as a mixture of a puzzle dependency graph and a walkthrough.
To keep the chart reasonably short, it assumes you explore every scene and pick up everything that isn't nailed to the wall (but we all do that anyway, right).
Bonus: This chart also contains the secret code to enable Box Mode.
The chart comes in the form of a PDF file allowing infinite zooming and text searching.