I've made a navigational tree that is ordered as the "ideal reading order" from beginner / advanced to knee-deep-into it.
The books listed are the ones I really consider the best ones in their overall area. Sometimes that means common topics will be skipped because a more specialized book is so much better that it saves a beginner from incomplete knowledge. I.e. there's no "bash" or "Unix shells" books, instead there's a selection of the best ones on Korn Shell (ksh) - almost anything you learn in there is applicable to the bash shell! The difference is that the ksh books really explain stuff and go to a much greater depth (whereas there are dozens of shell books which mostly aren't really great at teaching you the basics either)
Where I had the chance I've written something about the book in question, why I liked it or anything else to know about it.