The tool for visual programming

Answer 1

Check out Microsoft DSL Tools - http://msdn.microsoft.com/en-us/library/bb126259.aspx

It is a "designer generator" - allows you to define your own diagram format, specify shapes, arrows, colors, etc. and generates a designer for you that is able to edit such diagrams and export any textual artifacts about your diagram (e.g. XML or code).

Answer 2

What about using something like GraphWiz?

Answer 3

http://www.graphviz.org/

HTH