Prism 5 Help - Prism 5 does not come with manuals. Instead it has a very comprehensive Help system, that includes both information on using the program as well as help choosing and interpreting analyses, and detailed explanations of each built-in equation.
Prism 4 manuals - These four books/manuals come with Prism 4, and are freely available as pdf files. One set of manuals serves for both Windows and Mac users.
Intuitive Biostatistics - Straightforward statistics text written by GraphPad's Harvey Motulsky.