Linux
General
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