Hello:
I have a parcial solution for this but without using GlassPane.
In my application I ADD panels in my left side of my Split Pane, I can
add a rectangle component over the selected panel and drag that
rectangle... the problem is when I am releasing the mouse... the panel
did get the new position but I can't make the other panels to reorder
themselves, the panel I moved is over another one... how can I put the
panel in its new place an realign the others??

My application looks like this:
+---------+------------+

(Rectangle)            |

.---------.            |+

.---------.-------------

I have 3 classes and 1 main class:
- objLegend
- objPanel
- objRectangle

- objMainWindow

/*********this is the code for each class*******////
public class objLegend extends JPanel
{
    public Container container = new Container();
    public objMainWindow mainWindow = null;
    public int intTotalPanels = 0;
    public int intLastIndexPanel = 0;
    private Rectangle rec = null;
       
    public objLegend()
      {
           super(new GridLayout(0,1));
         
           setFocusable(true);
           setAutoscrolls(true);
           container.setLayout(new BoxLayout(container,
BoxLayout.Y_AXIS));
       
           JScrollPane scrollPane = new JScrollPane(container);
           add(scrollPane);
           show();
      }
   
}

public class objRectangle extends JComponent
{
    objPanel panel = null;
    objMainWindow mainWindow;
    Rectangle rec = null;
   
    public objRectangle()
    {   
        setBorder(BorderFactory.createLineBorder(Color.blue));
        setVisible(true);

   }
}

public class objPanel extends JPanel implements MouseListener,
MouseMotionListener
{
     
        JCheckBox objCheck;
       JLabel objLabel;
       public objMainWindow mainWindow = null;
       public int intOrder = 0;
       private static Rectangle rec = null;
       objPanel objP;
       
       public objPanel()
       {
           super(new BorderLayout());
   
           this.addMouseListener(this);
           this.addMouseMotionListener(this);
             
           objCheck = new JCheckBox();
           objCheck.setSelected(true);
   
           objLabel = new JLabel();
           objLabel.setText("Layer");
                   
           this.add(objCheck, BorderLayout.LINE_START);
           this.add(objLabel, BorderLayout.CENTER);
           this.add(objLabel, BorderLayout.SOUTH); //solo para hacer
bulto
         
           setBorder(BorderFactory.createLineBorder(java.awt.Color.black));
           
           this.show(true);
        }
       

       public void setOrder()
       {
           mainWindow.legend.intTotalPanels =  
mainWindow.legend.intTotalPanels + 1;
           this.intOrder = mainWindow.legend.intTotalPanels;
     
       }
       
       public void mousePressed(MouseEvent e)
          {
             //mainWindow.rectangle.hide();
             rec  = e.getComponent().getBounds();
             System.out.println("Pressed on: "+rec+" ");
             mainWindow.rectangle.setBounds(rec.getBounds().x,
rec.getBounds().y, rec.getBounds().width, rec.getBounds().height);
              //mainWindow.rectangle.show();         
            
            
          }
     
         
          public void mouseDragged(MouseEvent e)
          {
                rec  = e.getComponent().getBounds();
                mainWindow.rectangle.setBounds(mainWindow.rectangle.getBounds().x,
e.getY()+ (this.intOrder-1)*this.getHeight()+this.getHeight()/2,
mainWindow.rectangle.getBounds().width,
mainWindow.rectangle.getBounds().height);
              mainWindow.rectangle.show();   
          }
             

          public void mouseReleased(MouseEvent e)
          {
               Component c = mainWindow.getGlassPane();  
               c.hide();
         
               objP = (objPanel)mainWindow.map.get(this.getName());
             objP.setBounds(objP.getBounds().x,mainWindow.rectangle.getBounds().y,objP.getBounds().width,objP.getBounds().height
);
             mainWindow.rectangle.hide();
         
             System.out.println("Location: "+  this.getLocation());
             this.setLocation(mainWindow.rectangle.getLocation());
             

             System.out.println("Released:
"+mainWindow.rectangle.getLocation()+"  "+mainWindow.map.values());
           
             
          }  
         
          public void mouseClicked (MouseEvent e)
          {
              objP = (objPanel)mainWindow.map.get(this.getName());
              System.out.println("objPanel  "+objP.intOrder);
              mainWindow.intOrder = objP.intOrder;
          }
         
          public void mouseExited  (MouseEvent e) {}
          public void mouseMoved   (MouseEvent e) {}
          public void mouseEntered (MouseEvent e) {}

    }

public class objMainWindow extends JFrame implements ActionListener
{
 public static objMainWindow mainWindow = null;
 public JSplitPane sp = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
 
 public objLegend legend = new objLegend();
 public JPanel objViewer = new JPanel();  
 
 public JTextField textbox1 = new JTextField(20);
 
 public objRectangle rectangle;
 public objPanel panel;

 public HashMap map = new HashMap();
 
 public int intOrder;

   public objMainWindow(String header)
   {
                super(header);
       addWindowListener(new java.awt.event.WindowAdapter() {
           public void windowClosing(java.awt.event.WindowEvent evt)
{
               System.exit(0);
           }
       });
       setBounds( 300, 100, 700, 600 );
       initGUI();
       show();
       mainWindow = this;
       Dimension screenSize =
Toolkit.getDefaultToolkit().getScreenSize();
       Dimension windowSize = mainWindow.getSize();
       mainWindow.setLocation(Math.max(0,(screenSize.width -        
windowSize.width)/2),
               Math.max(0,(screenSize.height-windowSize.height)/2));
     
   }

/******more code******/

public void actionPerformed(ActionEvent e) {
       objPanel objPanelI;
       if ("add".equals(e.getActionCommand()))
       {
           panel = new objPanel();           
           panel.mainWindow = this;
           panel.setOrder();
             
           legend.container.add(panel);
           
           legend.intLastIndexPanel = legend.intLastIndexPanel + 1;
           panel.setName("objPanel"+legend.intLastIndexPanel);
           
           map.put(panel.getName(), panel);//
           
           panel.objLabel.setText(panel.getName());

           panel.setSize(new Dimension (130,71));
                                         
           System.out.println("added");
           Rectangle rec = panel.getBounds();
           System.out.println("PANEL: "+rec);
           sp.revalidate();
         
           
       }
   }

/****more code****/

/****more code****/

   public static void main(String[] args) throws Exception
     {
       UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
       new objMainWindow("Paneles");
     }

}

/*****the end********************************************************************/

I posted another "Follow up" before with the source code... this is
the missing code for the objMainWindow class:

   private void initGUI() {
     
        JButton boton = new JButton("ADD");
        boton.setActionCommand("add");
        boton.addActionListener(this);
       
        JButton boton2 = new JButton("Get Top");
        boton2.setActionCommand("gettop");
        boton2.addActionListener(this);
       
        JButton boton3 = new JButton("Set Top");
        boton3.setActionCommand("settop");
        boton3.addActionListener(this);
       
        JButton boton4 = new JButton("Remove");
        boton4.setActionCommand("remove");
        boton4.addActionListener(this);
       
        objViewer.add(boton);
        objViewer.add(boton2);
        objViewer.add(boton3);
        objViewer.add(boton4);
        objViewer.add(textbox1);
   
        rectangle = new objRectangle();
        legend.setAutoscrolls(true);
       
        legend.container.add(rectangle);
       
        sp.setTopComponent(legend);
        sp.setBottomComponent(objViewer);
       sp.setDividerLocation(130);
       
       getContentPane().add( sp, BorderLayout.CENTER );
       
       
   }