Three more good ones:
. It's oriented to Ubuntu, but it's full of good info.
. Machtelt Garrels's Intro to Linux. I printed it out and still have it on my bookshelf. If had to pick the one book that helped me the most when I was new, this would be it.
. Slackware oriented and in need of updating, but excellent on the basics, such as file structure, permissions, and the like.