Jario64, the Java Nintendo 64 Emulator now has an audio plugin. Go to the downloads section and try it out.

Also new in this version of Jario64 is a frame limiter (so audio will stay in sync) and some minor performance enhancements. You can toggle the audio and frame limiting on/off in the settings menu before the game starts. The audio plugin is implemented with the standard Java Sound API and is threaded (so at least a dual core cpu is recommended for running audio). If your framerate is too low (below about 50 fps) then the audio will start to get choppy and distorted just as the frames will visually start to seem choppy below 30 fps.

Also provided in the download section is a ready to run downloadable package for Windows x64 in addition to the webstart launcher. This package can easily be modified for other operation systems by replacing the JOGL files with the appropriate ones for you system and creating a script to launch the application.