This is a quick hack to be able to produce http://d3js.org force layout with a third dimension. I use two force layouts in combination, the first one for the x,y axis and the third one for the z axis (I enforce x=y at each step). Each chained action of the 3d force is then applied to both of the underlying forces. Finally I use X3DOM to render the visualization.
List of controls can be found here http://www.x3dom.org/?page_id=293