You can find a wealth of resources at The Linux Documentation Project
My most useful references came from there. I know that sometimes nothing beats a book; the ones I found most useful I downloaded as PDFs and printed. I have about five of them in big white binders on my bookcase right now.
Then there's the Slackbook. http://www.slackbook.org/
. Slackware oriented, but excellent on the basics, such as file structure, permissions, and the like.