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 ...

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

If you find your thrill delving into the networking side of Unix, you'll find that there are lots of commands to give you all the insights you might want.