Well, one book you should definately have Unix in a Nutshell by O'Reilly (the BEST unix command book around). Other ones I'd recommend:

Running Linux (another O'Reilly)
A Practical Guide to Unix System V by Sobell
Unix System Administration Handbook (3rd Edition)

I've also found Linux Administration: A beginner's guide, Solaris Administration: A Beginner's Guide and Red Hat Unleashed.