Answer
Most PDFs included in ArcGIS 9.1 and above Esri Software Documentation Library are available in:
<install_location>\ArcGIS\Documention
All topics that were covered in the PDF books included in the Esri Software Documentation Library at version 9.1 and above that are not in C:\Program Files\ArcGIS\Documentation have been included directly into the ArcGIS Desktop Help.
If any topics in the Esri Software Documentation Library are not available in ArcGIS Desktop Help, please submit this as a bug to Esri Support Services.