One of my personal favorites are Kernighan & Pike's The Unix Programming Environment but it's very old, so some of the peripheral details have changed quite a lot since then. Another perennial is Friedl's Mastering Regular Expressions, although you might struggle with it at first if you are not familiar with the tools it covers.

The O'Reilly sed & awk book is a good introduction to sed and awk, although there are a lot of on-line tutorials which are probably just as good.

The FAQ section has more links; I'm new to Unix. Which books should I read? - The UNIX Forums