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I just created a variation of the D3.js Sankey diagram to visualize the many-to-many relationships between the stacks of the entities, that I want to use for enterprise architecture application. It does what you wanted and much more.
Here is the gist:
https://gist.github.com/colinyzhao/5649114
and the demo
http://bl.ocks.org/colinyzhao/5649114
The height of the node is based on node value. The link has two values, sourceCount (value) and targetCount. The node has three more fields to further constraint the width of the link/path calculation. Links can overlap at the source and target node.