Analysis

Aubio
API and command line tools for audio analysis (segmentation, pitch and beat detection).
http://aubio.org/

CLAM
Software framework for research and application development on the audio and music domain. Provides means to perform complex audio signal analysis, transformations and synthesis.
http://clam-project.org/

FEAPI
Feature Extraction plugin API.
http://feapi.sourceforge.net/

jAudio
A Java software package for extracting features from audio files as well as for iteratively developing and sharing new features.
http://jmir.sourceforge.net/jAudio.html

libsms
Open source C library that implements SMS techniques (sinusoidal plus residual model) for analysis, transformation and synthesis of musical sounds.
http://mtg.upf.edu/technologies/sms?p=libsms

LibXtract
Open source, portable, lightweight library of audio feature extraction functions.
http://libxtract.sourceforge.net/

Marsyas
Open source software framework for audio processing with specific emphasis on Music Information Retrieval applications.
http://sourceforge.net/projects/marsyas/

Praat
Program to analyze, synthesize, and manipulate speech, and create high-quality pictures from the results. But it can be used for other types of sounds as well.
http://www.fon.hum.uva.nl/praat/

Sonic Visualizer
Framework for audio signal analysis.
http://www.sonicvisualiser.org/

Tapestrae
Analyzes and recomposes sound scenes.
http://taps.cs.princeton.edu/

WaveSurfer
Open source tool for sound visualization and manipulation. Typical applications are speech/sound analysis and sound annotation/transcription.
http://sourceforge.net/projects/wavesurfer/


File Formats

libsndfile
C library for reading and writing files containing sampled sound.
http://www.mega-nerd.com/libsndfile/

SoX
Cross-platform (Windows, Linux, MacOS X, etc.) command line utility that can convert various formats of audio files into eachother.
http://sox.sourceforge.net/


IO

oscpack
Simple C++ Open Sound Control (OSC) packet manipulation library.
http://code.google.com/p/oscpack/

PortAudio
Cross-platform and open-source audio I/O library.
http://www.portaudio.com/

rtAudio
Set of C++ classes that provide a common API for realtime audio input/output across Linux, Macintosh OS-X and Windows (DirectSound and ASIO) operating systems.
http://www.music.mcgill.ca/~gary/rtaudio/

rtMidi
Set of C++ classes that provide a common API for realtime MIDI input/output across Linux (ALSA & Jack), Macintosh OS X, Windows (Multimedia Library), and SGI operating systems.
http://www.music.mcgill.ca/~gary/rtmidi/


Modular Synthesis

CSound
Programming language for sound rendering and signal processing.
http://www.csounds.com/

PureData (PD)
Real-time graphical programming environment by Miller Puckette. One of the best prototyping tools.
http://puredata.info/

libpd
libpd is Pure Data as an embeddable library.
https://github.com/libpd

STK
Open source audio signal processing and algorithmic synthesis classes written in C++ by Perry R. Cook.
http://ccrma.stanford.edu/software/stk/