I was searching for a way to make Java inoperable with .net and activex on windows. Here are a few links that you might find interesting.
Hosting .NET Controls in Java
Hosting .NET Controls in Java (Print Edition)
Java Native Interface (JNI) - adding an ActiveX to a Canvas
Hosting ActiveX/.NET controls in a Java Application.
Making Native Windows API calls from within a Java Application
Make a Window "stay on top"
The last two links shows you how to get the hwnd of a window and make it stay on top. The DJ Project allows you to mix heavyweight and lightweight components. so you can actually use flash animations in your Java project.