How does one download the CiviCRM 4.6 User Guide in PDF?
Looks like PDF isn't available, but a downloadable copy of those docs in Markdown format is available from the Github repository linked in the top right of http://docs.civicrm.org ("Edit in Github").

github.com/civicrm/civicrm-user-guide => Download ZIP

This (zipped) download is in a quite readable format, even in a plain text editor. Which tool you view it in will determine whether some features like inline images are displayed; search for a Markdown editor for your OS if you want support for images / visual formatting.

Bonus: it's a great format to submit docs fixes! Perhaps your first submission will improve on "This book is freely available to read online and download in multiple formats." in docs/index.md :)

In that linked Github repo, you'll see a mkdocs.yml file indicating that CiviCRM's docs are built via MkDocs. According to this FAQ answer on readthedocs.org,  the Markdown/MkDocs format doesn't provide us with automatic PDF generation (yet) but it does make it easy for people to contribute improvements.