Audio Recording/Editing
Audacity
Ardour
Wavesurfer
Wavosaur (Windows only)
Audio Programming Languages
Pure Data
ChucK
Faust
SuperCollider
Nyquist
Csound
Alda
Synthesis
Paulstretch standalone, Paulstretch VST
Interactive Source Separation Editor (ISSE)
Spear
Tapestrea
High C
Inter-application Audio Routing
Soundflower (OSX only) [tutorial]
Jack [tutorial]
Movavi Audio Capture (free demo)
Windows users might also have luck using Audacity and the WASAPI option.
Plugins
EchoThief
Soundhack
Soundmagic Spectral (OSX only)
KVR
VST Planet
Misc
Planet CCRMA (Linux audio suite)
Sndpeek (audio visualization)
ReacTIVision (video tracking software)
SoX (file format converter)