Yeah, I noticed JFugue a few years ago. It's on my list of interesting computer/music bookmarks:
http://delicious.com/BenjiSmith/computermusic
http://delicious.com/BenjiSmith/programming.java.libraries.music
But JFugue is all about the structure of the music itself... the melodies, harmonies, rhythms, etc....
What I'm looking for right now is just the synthesizer. Something like this...
Synth s = new Synth();
Instrument i = s.getInstrument("Robot Bass");
i.makeAwesome(true);
And then I'll send my events into the MIDI stream (or into whatever control API the synth library provides).