Pierre Dragicevic has a very interesting idea to solve the problem of drag and dropping an element across overlapping windows. Despite a few quirks his Java demo is really interesting to run. I wish the code was open to improve the visual quality of the rendering. It seems, given the size of the class files, it's a hell lot of code though.
You can also read his article for more information about the idea and the implementation. I wish I had this idea before him ^^