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 ...

Need a jump start on Unix networking? Whether you're working on your home network or setting up systems at work, here are some basic Unix networking commands and insights that might prove helpful.

Providing only the basic commands that jailed users need is not quite enough, however. While it might not be obvious, most basic Unix commands are incomplete in themselves.