Spectral Processing
Chapter 3 of Music and Computers from Columbia University provides a good and accessible explanation of sound in the frequency domain
and, chapter 5 explains some spectral transformation techniques including convolution and the phase vocoder.
This section of the Pd-tutorial explains about frequency domain and some aspects of spectral processing.
Explanation of convolution from Barry Truax.
Discussion of convolution for reverb and sound design.
Mark Dolson's article on the phase vocoder (from Computer Music Journal) explains the theory and application of this technique
Fons Adriaensen's LAC paper on convolution engine for reverb provides a very good discussion of natural reverb and convolution.
A very good set of tools for spectral processing is soundhack (including Pd/max externals you can download - look under freeware).