hmm, thought you could do that without MIDI in Java (Though, I don't like/use Java so I wouldn't know)
If you want this to run on Linux, then that won't work with MIDI - Unless the hardware and drivers both literally support it, which does not occur very often. (Usually its done on software) I'm not sure about Mac OSX, but i think it will play fine there (QuickTime plays them, i think, and some of MacOSX's core audio uses QT, if i remember properly)
Anyways, I don't know of any GB emulators that use MIDI and are open source, Java or not. Thats a very specific query.