Reference

http://www.gnu.org/ The website of the GNU project, it contains manuals and downloads for lots of command-line software.

http://www.linuxdevcenter.com/linux/cmd/ A wide selection of Linux commands and explanations of what they do.

http://www.tuxfiles.org/linuxhelp/cli.html Several short command-line tutorials, courtesy of tuXfiles.

http://www.linuxcommand.org/ Describes itself as "your one-stop command line shop!" It contains a wealth of useful information about the console.

http://www.tripwire.org Information and download links for the open-source version of Tripwire.

Books

Understanding the way UNIX works at the nuts and bolts level can be both challenging and rewarding, and there are several good books that will help guide you on your way. Perhaps the best is The Art of Unix Programming by Eric Raymond (Addison-Wesley, ISBN: 0-13-142901-9), which focuses on the philosophy behind UNIX and manages to mix in much about the command line.

O'Reilly's Unix CD Bookshelf (ISBN: 0-596-00392-7) contains seven highly respected books in one, although it retails for more than $120 as a result! That said, it is incomparable in its depth and breadth of coverage.