• The Linux Documentation Project (TLDP)
• Updates on this site have slowed, so it is mostly useful for information on established parts of the Linux system, and for basic introductions. It offers its guides in a variety of formats.  Below, I generally link the on-line HTML version, but you can go back and pull other formats from the home page of the guide.
• Introduction to Linux (TLDP), Machtelt Garrels, 2008.
• UNIX Tutorial for Beginners, by M.Stonebank AT surrey.ac.uk (thanks to Adam Luck for pointing out this site)

The bash Shell

• Bash Guide for Beginners (TLDP), Machtelt Garrels, December 2008.
• Advanced Bash-Scripting Guide (TLDP), Mendel Cooper, March 2014.
• bash Cookbook (available on ProQuest Safari Books On-Line)
• By: Carl Albing; JP Vossen; Cameron Newham
• Publisher: O'Reilly Media, Inc.
• Pub. Date: May 24, 2007
• Print ISBN-13: 978-0-596-52678-8, Print ISBN-10: 0-596-52678-4