QuantumPortal
Free software "Blending algorithmic techniques with contemporary Music Theory to "air brush" compositions."
http://quantumportal.com/

Frameworks and Environments
Academic paper defining data structures for general concepts of composition, sound synthesis, networks.
http://www.ircam.fr/equipes/repmus/RMPapers/Hanappe97/

GrooveLab
Make your drum loops online.
http://artopod.com/groovelab/

ARiADA Project
Researches composition strategies for electroacoustic music.
http://www.ariada.uea.ac.uk/

AudioMulch
Interactive musician's environment offers music composition by sound synthesis and "contraptions".
http://www.audiomulch.com/

Swar Systems
Create music using Indian melodies and scales. Supports up to 8 instruments.
http://www.swarsystems.com/

Ixi Software
Prototypes and apps for composition of experimental music.
http://www.ixi-software.net/

Compo
Composition system based on common LISP, generates MIDI and scores.
http://compo-music.net/en/accueil.php

Virtual Studio Systems
Offers Lyricist and TrackNotes for musicians, songwriters, and home recording.
http://www.virtualstudiosystems.com/

TaalMala and SwarMala
Compose Taal (loops) with Tabla and Pakhawaj (Indian drums). Export to WAV or MP3. Also offers the SwarMala sequencer.
http://taalmala.com

Pymprovisator
For jazz. Set song parameters and program generates MIDI file with adequate accompaniment. Freeware.
http://pymprovisator.sourceforge.net

Chord Arranger Pro
Creates styles from any MIDI file and is able to identify chords and convert song measures into style parts.
http://www.xdigits.com/midi/rmca.html

Drumsite
Drum track creation tool, supports multiple samples and effects.
http://www.guitar.sk/drums/drums_main.htm

ComposerTools.Com
Free on-line tools including 12-tone row analysis and pitch class. Also "MusicGraph" a tool for graphing music across dimensions.
http://composertools.com

Hard Note JUMP
Streamlined MIDI sequencer that focuses on composition rather than audio production. Demo available.
http://hardnote.com

Rhythm Rascal
Create drum tracks using any sample WAV files as drum sounds. Flexible, although designed mostly for Rock and Metal.
http://www.rhythmrascal.com

The Palette
Melody composing tool uses composition and harmony theory to help composers develop phrases, sentences, periods, and motifs.
http://www.palette-mct.com

SmartSound Software, Inc.
Sonicfire Pro 4 with Mood Mapping, music scoring software, and royalty-free music for video productions.
http://www.smartsound.com