I was looking for tools to draw area-proportional Venn Diagram, but most of them either do not work in some cases or very difficult to use. Finally, I found a very very good one!

A very very nice tool to draw Area-Proportional Venn Diagram:

http://bioinforx.com/free/bxarrays/venndiagram.php

I can also edit the Venn Diagram including labels, size and positions:

So far this is the best I found on the web.