<p><em>With the popularity of the Apple iPhone, the potential of the Microsoft <a href="http://www.microsoft.com/surface/index.html" rel="noreferrer">Surface</a>, and the sheer fluidity and innovation of the interfaces pioneered by Jeff Han of <a href="http://link.brightcove.com/services/link/bcpid713271701/bclid713073346/bctid709364416" rel="noreferrer">Perceptive Pixel</a> ...</em></p>
<h3>What are good examples of Graphical User Interfaces which have evolved beyond the</h3>
<h3>Windows, Icons, ( Mouse / Menu ), and Pointer paradigm ?</h3>

Are you only interested in GUIs?  A lot of research has been done and continues to be done on
tangible interfaces
for example, which fall outside of that category (although they can include computer graphics).  The
User Interface Wikipedia
page might be a good place to start.  You might also want to explore the
ACM CHI Conference
.  I used to know some of the people who worked on zooming interfaces; the
Human Computer Interaction Lab an the University of Maryland
also has a bunch of links which you may find interesting.
Lastly I will point out that a lot of innovative user interface ideas work better in demos than they do in real use.  I bring that up because your example, as a couple of commenters have pointed out, might, if applied inappropriately, be tiring to use for any extended period of time.  Note that light pens were, for the most part, replaced by mice.  Good design sometimes goes against naive intuition (mine anyway).  There is a nice
rant
on this topic with regard to 3d graphics on
useit.com
.