Japhar is different because it was designed from the
beginning to conform to the JNI Spec published by Sun. So,
it's easy to actually embed Japhar in your own programs (you
can even create more than one Japhar VM in the same process.)
Performance is important to us, but it is secondary to our primary goal, which is to very quickly follow specifications as they are published. We have, for example, begun work on following the Java VM Debugger Interface (JVMDI). The goal is to hook up GDB to this interface to provide a consistent debugging environment.
That being said, there are plans to work on a JIT for japhar. Please contact email@example.com for more info, or if you'd like to help out (or write the entire thing :)
Also, japhar uses thread libraries that are native to the machine. Both pthreads and cthreads are supported.