PS: It is not possble with Java3D because Java3D is heavyweight and Swing is leightweight. The problem then is that Pop-up/menus go behind the 3d component.
If pop up menus are your only problem, then theres a flag to force menus to be heavyweight ( http://www.j3d.org/faq/swing.html
). Xith (and indeed any hardware accelerated 3d engine) uses a heavyweight component which will cause the usual depth ordering problems.
If you really need a lightweight 3d display, then perhaps jPCT will do what you want ( http://www.jpct.net/