This book is a little more distro specific, but I really liked the Red Hat Linux Bible. Linux in a Nutshell has just about every command out there for Linux (it's quite a read).
A long time ago, there was this PDF floating around called "UNIX is a Four Letter Word". That was quite good, but tries to be specific to the C shell which I doubt you will be running any time soon. But, a lot of the command wills work on Bash as well. If you can't find it, PM me and I'll send you a copy of that.