Only Swing components (as far as I can tell). I'm trying to get used to the code myself (I'm new on this project).
I'll work on an example tonight. Basically, we are trying to get a modal JInternalFrame. For that, we create a non-opaque glass pane on the JFrame that captures all mouse events. Then we create a JInternalFrame inside of that. This JInternalFrame acts as a modal frame because no other frames can get the focus. But the JComboBox inside that JInternalFrame has its popup behind the glassPane ...
Well, yes, the glass pane sits over the layered pane (which contains the popup layer used by the combo dropdown) - so if you place components directly into that then all the others will be behind them.
I expect this explains it in more detail,
http://java.sun.com/docs/books/tutorial/uiswing/components/rootpane.html