I have succeeded in directly compositing my graphics engine to a vista window, using a dynamic DLL load so it doesn't cause any problems on XP. I also managed to create a situation where the window is entirely transparent and impossible to click, which was an absolute bitch to get working. For future reference, if you ever want a window that is click-through, use CreateWindowEx with both WS_EX_TRANSPARENT and WS_EX_LAYERED. Using only one will not work, nor will any sort of windows message handling. That is the ONLY WAY to make the window click-through. Consequently to do opacity based hittesting, you have to hook the mouse events for the entire desktop and manually notify your window after doing the calculations yourself (something I don't even want to think about).
There are other options and you don't get to see the subtle adjustments I make to whether or not a window is draggable, or if its clickthrough etc, but it gives you a rough idea.
Now, on to stencil buffers and masking and maybe i'll release this thing only a week late! FFFFFFFFFFFFFFFFFFF-