Linux

AlsaPlayer
PCM player written for ALSA driver and library, supports other outputs like OSS and esd. Plug-in interface.
http://www.alsaplayer.org/

Audio File Library
An API for accessing a variety of audio file formats.
http://www.68k.org/~michael/audiofile/

Aumix
Adjusts an audio mixer. X and ncurses interfaces.
http://jpj.net/~trevor/aumix.html

Baudline Signal Analyzer
Realtime signal analysis and spectrum analyzer tool.
http://www.baudline.com

BEAST/BSE
GTK+/GNOME based front-end to BSE framework to simulate audio synthesis and tracking composition.
http://beast.gtk.org

Cdgtools
Suite of tools for handling CD+G karaoke disks and files.
http://www.kibosh.org/cdgtools/

CoverViewer XMMS Plugin
Displays covers or images related to songs. Internet cover retrieval facility. Handles tagged files, CDs, and streams.
http://coverviewer.sourceforge.net

Dir2ogg
Python script that converts MP3, WAV, and M4A files to Ogg format.
http://badcomputer.org/unix/dir2ogg/

Ecasound
Audio software for Unix.
http://www.eca.cx/

Geoff and Dave's Audio Mixer
A digital audio mixing package.
http://gdam.ffem.org/

GLAME
Free and extensible Linux/Unix audio editor. GNU licence.
http://glame.sourceforge.net/en/index.var

GNOMAD
GTK+ client program for the NOMAD Jukebox, using libnjb and id3lib to handle communications and ID3 tagging.
http://www.df.lth.se/~triad/krad/gnomad/

Gnome Wave Cleaner
An audio cleanup tool for GNOME. Handles WAV, MP3, and Ogg.
http://gwc.sourceforge.net/

GramoFile
Assists in moving gramophone records onto CDs. Filters out hiss and pops.
http://www.opensourcepartners.nl/~costar/gramofile/

Grip
Cd-player and cd-ripper. It also provides an automated frontend for MP3 and other audio format encoders.
http://nostatic.org/grip/

KGuitune
A program for tuning guitars and other instruments that is available for download.
http://www.geocities.com/harpin_floh/kguitune_page.html

Lilypond
Creates beautiful music notation from text input. Outputs Postscript, SVG or MIDI files. GNU license.
http://lilypond.org/web/

Linux Sampler Project
Audio sampler with features similar to hardware samplers. Offers speed, high audio quality rates, supports common sample library formats.
http://www.linuxsampler.org

Mixxx
Open source DJ mixer.
http://mixxx.sourceforge.net

MusE
MIDI/Audio sequencer with recording and editing capabilities.
http://www.muse-sequencer.org/

Orpheus
Text and window mode audio player for CDs and MP3 with CDDB interface.
http://konst.org.ua/orpheus

Philip's Music Writer
A music typesetter. Input is a plain text file, output is in PostScript.
http://www.quercite.com/pmw.html

PyKaraoke
CDG/MP3+G karaoke player. Can search inside Zip files.
http://www.kibosh.org/pykaraoke/

Rosegarden
MIDI sequencer and notation editor for Unix-like systems.
http://www.rosegardenmusic.com/

SndStretch
Plug-in for XMMS to adjust pitch and tempo of a sound.
http://www.geocities.com/harpin_floh/sndstretch_page.html

Sound Processing Kit
An object-oriented class library for audio signal processing.
http://www.music.helsinki.fi/research/spkit

SoundTracker
MOD tracker for X, similar to FastTracker. Includes a sample recorder and editor.
http://www.soundtracker.org/

The TAON Project
A sound editor for Linux.
http://www.informatik.uni-frankfurt.de/~eschenb/taon/

TiMidity++
MIDI player, converter to wav. Uses Gravis compatible patches and can play these through soundcards lacking their own patches.
http://sourceforge.net/projects/timidity/

XMMS-SID SIDplay Plugin
Plug-in for playing Commodore 64 music (SID tunes) with XMMS. Requires libSIDPlay library (link given).
http://www.tnsp.org/xmms-sid.php

xmp: Extended Module Player
Open source (GNU GPL) portable module player for Unix or Win32.
http://xmp.sourceforge.net/

Zero Tolerance's Cue Creator
A small Perl script that allows you to create CUE and MP3/OGG/WAV-files from audio CD's.
http://www.x-a.be/index.php?page=14

ZynAddSubFX
Synthesizer with two engines, realtime polyphonic, Midi support, microtonal capability, effects.
http://zynaddsubfx.sourceforge.net