Tools

Freeware/shareware

Supercollider (Linux, Mac OS X, free) - a very sophisticated real-time synthesis and composition language. The text-based language is loosely-typed and supports closures, making it similar to LISP or Scheme and very useful for manipulating sets and sequences. In addition it supports multi-threading, multi-processing, and even client-server distributed processing. Its major problems are instability and incomplete documentation, so it has a near-vertical learning curve.

AudioMulch (Windows, $50 shareware) - a visual programming language for real-time audio processing with MIDI control. Provides a set of interesting audio processing modules which you can plug together and control. You can also drop VST plugins in and use them as modules. AudioMulch makes it easy to quickly throw together complex signal processing processes and control their parameters from MIDI control sources, making it useful for performance and improvisation.

SoftStep (Windows, $129 shareware) - a visual programming language for real-time MIDI composition and processing. Can be used as a source of control information for AudioMulch. One of the most unusual features of SoftStep is its support for microtonality through precise pitch-bend twiddling. My big gripe with it is that its interface is poorly designed, making complex patches hard to manage.

soundhack (Mac OS 9.2/X, free) - extremely high-quality non-realtime spectral processing. Useful for time-stretching and spectral dynamics processing.

bosch/bisch (Linux, Mac OS X, not released) - my own tool. No interface, no documentation. Use Coagula instead.

destroyfx plugins (Windows, Mac OS, free) - Useful for randomly chopping audio signals into small subsegments, bridging the gap between granular synthesis and turntablism.

Commercial