If you're not yet comfortable with writing scripts on Unix and Linux systems, this post might get you off to a healthy start.

The O'Reilly book (Learning Unix for OS X) is decent, but it doesn't really get into OS X-specific things. It doesn't even cover Homebrew. IIRC the only exception is a section on the md* commands ...

Our Linux cheat sheet includes some of the most commonly used commands along with brief explanations and examples of what the commands can do.