I'm a little late, but let me put in my two books' worth, both from O'Reilly:Running Linux
by Matt Welch, Lar Kaufmann, and Matthias Kalle Dalheimer - I believe this is available in .pdf format from O'Reilly's Safari site (not to be confused with the browser of the same name). There have been at least four editions of this book and it just keeps getting better. It is more of a broad overview of all things Linux than it is just a command line guide, but it's worth having in your library if you're serious about learning Linux.
(to the new 5th Edition!)Linux Pocket Guide
by Daniel Barrett - this is the book you literally want in your back pocket. I have my copy tabbed out for quick reference. If you want to know how to do something at the command line, this book will at least get you started, and most times will get you finished quicker than anything else I've read.
They also publish a Linux Desktop Pocket Guide, but I haven't held that one in my hands yet. I'll be looking for it, though. The pocket guides are cheap (usually around ten bucks American) and designed to fit in the back pocket of a pair of Levis jeans easily.