new IWorkbenchListener{
     @Override
        public boolean preShutdown(final IWorkbench workbench, final boolean forced) {           
            if (forced) {
                return true;
            }
            //Logic here to determine if we really want the workbench to close.
        }
}

new IWindowCloseHandler {
   @Override
   public boolean close(final MWindow window) {
       //Logic here to determine if we want the window to close.
   }
}