I think you could write a little class, extended
from Thread, which will be responsible to call your
other application, like this

public class Caller extends Thread {
public void run() {
String[] parameters = new String[0];
OtherApp.main(parameters);
}
}

and then call it from your calling class:

new Caller().start();

Of course, the other app  must be in the main
application classpath. I think this shuld work