In Mustang methods JMenu.addSeparator() does actually nothing under GTK. It worked with 1.5.x JDKs. Try the following code:

        UIManager.setLookAndFeel("com.sun.java.swing.plaf.gtk.GTKLookAndFeel");
        JFrame f = new JFrame();
        JMenuBar mb = new JMenuBar();
        JMenu menu = new JMenu("Separator Menu");
        menu.add(new JMenuItem("1"));
        menu.add(new JSeparator());
        menu.add(new JMenuItem("2"));
        menu.addSeparator();
        menu.add(new JMenuItem("3"));
        mb.add(menu);
        f.setJMenuBar(mb);
        f.pack();
        f.setVisible(true);

There is not separator between 2 and 3. JMenu.add(new JSeparator()) may be used as a workaround - it works.