For programming in Unix, Eric Raymond's _The Art of Unix Programming_ is essential. While it has its flaws, this book does a good job describing the philosophy and typical architectures of Unix programs. I particularly liked his discussion of various data file formats.

If you're on Linux, another essential book is Kerrisk's _The Linux Programming Interface_. In-depth explanation of the APIs and examples of how to use them.

A quirky but personal favorite on programming in general is P.J. Plauger's _Programming On Purpose_. It's an OLD book from the days of structured programming and is focused mainly on data transforms a la data flow diagrams (DFD's). I've found it to be a useful way to think about shell pipelines, but also how to structure a traditional program consisting of a main module and subroutines. His bit about lifting up one of the bubbles from the DFD and letting the other bubbles fall below it as its subroutines has always stuck with me -- along with his analysis of how which bubble you choose affects program structure.

(By the way, I highly recommend learning something about those old structured design techniques and DFD's in particular. It will shed a lot of light on Unix's pipes-and-filters model -- and also, oddly enough, prepare you for the more esoteric world of functional programming.)

Ousterhout's new book _A Philosophy of Software Design_ is also good, although I didn't find every chapter as useful as others. A little too object-oriented for my taste. But excellent advice on modular design.