Wall, Larry & Christiansen, Tom & Schwartz, Randal; O'Reilly; 1997;
ISBN 0-56592-149-6; 644pp.
Shell (as a programming language for more than trivial scripting) is dead. Perl rules in its place. This is the second edition of the definitive Perl book -- vastly better organized than the first, and it covers Perl 5.
Lutz, Mark; O'Reilly; 1997; ISBN 0-56592-197-6; 880pp.
The next step beyond Perl. Python is beautifully designed, has better integration with C, and scales up better to large projects.
Musciano, Chuck & Kennedy. Bill; O'Reilly; 1997;
ISBN 0-56592-235-2; 552pp.
The best HTML tutorial/reference I have ever seen, and the only HTML book you need unless you want to do CGI.
Kernighan, Brian, and Pike, Rob;
Prentice-Hall; 1984; ISBN 0-13-937681-X; 1984.
A true classic -- possibly the best single-book exposition of the Unix philosophy.