To my surprise, I found many of my personal favorites to be missing from the book recommendations thread.
Although dated, Kernighan & Pike's The Unix Programming Environment is a classical introduction, covering the shell, the scripting languages, make, troff, and some fundamental C programming concepts, in a distinctive "Bell Labs" style, by two pivotal figures in the history of Unix.
Jeffrey Friedl's Mastering Regular Expressions is a must for anybody who uses scripting languages. It is suitable even for beginners, although you have to be serious about regular expressions to read it cover to cover.
Eric Raymond's The Art of Unix Programming attempts to teach not only programming, but the philosophy and mind-set of the Unix masters. Although if it is mainly about "real" programming languages, it is worth a read even if you are only into scripting languages.
Kernighan and Pike's The Practice of Programming has examples in both systems priogramming languages (C and Java) and in scripting languages (Perl, TCL, awk, etc). Like the previous one, this book is more about mindset and philosophy than about any particular programming language. Another classic from the duo who wrote The Unix Programming Environment.
(The cover art is not particularly convincing, as such.)