Both the documentation and the molecules themselves are available from the Ventana Systems, Inc. Web site in the "Software" section.
Documentation
This document explains each molecule and has hyperlinks to related molecules. The document is organized so that it can be read from the beginning to the end and Prof. Jim Hines recommends doing that. There is also an alphabetical index of the molecules in the form of Adobe® Acrobat bookmarks, so that the document is well suited to being used as a reference as well.
Molecules
These are the molecules themselves, which are compatible with the Vensim® software by Ventana Systems, Inc. Unzip this file anywhere (unzipping it into the same folder that holds the Vensim® executable is a fine idea). Unzipping the file will give you a folder called Moleculesv2 which will contain all the molecules. After unzipping, open Vensim®; click on Windows>>molecules and navigate to the file called "molecule.mdl" within the Moleculesv2 folder. (Note if you have already installed a version of the molecules you will need to select Windows>>molecules twice. The first time will open your current version of the molecules, the second time will allow you to navigate to the new version).