From O'Reilly Press, and I must have made this same post a number of times... Tim O'Reilly owes me a kickback by now:
Running Linux, Matt Welsh, 3rd Ed.
Linux in a Nutshell, Ellen Seiver, 2nd Ed.
Running Linux covers a ton of just the general logic behind how the shells work, how the file systems are put together, how to install from source, make back-ups, plus a bunch of useless garbage... honestly how many people use tape drives any longer? Its written high enough level to be tough, but not something that only an experienced geek can understand.
Nutshell is basically a dictionary of commands that goes far enough beyond the sometimes poorly written man pages so as to be almost a must-have.
The other best reference: The source
, which has set up my bleeding edge wireless gear, hacked me through a dozen apache troubles, and been the source of numerous tricks.