I came across the second edition of the Prentice Hall’s “A Practical Guide to Linux Commands, Editors, and Shell Programming” by Mark G. Sobell (original link). This is a rather lengthy book at just over 1,000 pages, covering everything from history of Linux and basic commands, all the way to bash, Perl, and sed, and how things work both on the inside and outside.
It’s probably not one of those books to read from cover to cover, but quite handy to keep as a reference and flip a few pages once in a while.