Audacity [free multi-platform, multi-track audio editor]
Audacity plug-ins [at sourceforge]
Audacity plug-ins [David Sky]
SoundHack [audio mangler; Mac only]
PD [Mac/MSP-like; cross-platform]
Amadeus Pro [audio editor; Mac only]
Audio Hijack [capture audio from any computer source; want to capture the weird noises you get while scrubbing in Pro Tools?; Mac only]
Max/MSP [the king of interactive software; cross-platform]
Reaktor [powerful, programmable synthesis environment; friendly GUI; cross-platform]
Pro Tools [industry standard audio editor; requires specific audio hardware; costs vary from $300 to $30,000; cross-platform]
Digital Performer, Logic [high-end MIDI/Audio sequencers; Mac only]
Cubase [high-end MIDI/Audio sequencer; Cross-platform]
Sonar [high-end MIDI/Audio sequencer; PC only]