JavaZoom
Java MP3 Player supports WAV, AU, AIFF, Ogg Vorbis also.
http://www.javazoom.net/

JavaTuner
Tunings and temperaments. Demo applet.
http://pages.globetrotter.net/roule/accord.htm

jOggPlayer
Gui Enhanced Vorbis Ogg Player. Freeware.
http://joggplayer.webarts.bc.ca/

FreeTTS Speech Synthesizer
Written in Java, based upon Flite 1.1: a run-time speech synthesis engine from Carnegie Mellon. Open source, BSD.
http://freetts.sourceforge.net/docs/index.php

Neuralsemantics Modulator Jane
Applet uses standard AU sound files to modulate graphics on web page. Also offers Neurosonic e-Guitar.
http://neuralsemantics.com/mjane/mjprod.html

JFugue
API for specifying music using simple strings and easily transforming patterns of music.
http://www.jfugue.org

RPitch
Relative pitch ear training to recognize intervals. Freeware.
http://rpitch.sourceforge.net

FreeMusicPlayer
Part Java part native, supports MP3, WAV, Ogg, and playlists. Windows 2000/XP.
http://patriot.net/~gary/FreeMusicPlayer.html

Frinika
Cross-platform music studio software written in Java. Includes sequencer, software synths and realtime effects.
http://www.frinika.com