Graphviz is definitely suitable for what you ask. At the moment, the main site graphviz.org is not working yet, but someone kindly reflected the gallery examples (with source) Flickr.
http://www.flickr.com/photos/kentbye/sets/72157601523153827/
As far as I know, you cannot create “templates”, but you can do something similar for circles:
node[shape=circle, color=white, style=solid]; node1;node2;node3;
This will define the node (think of it as a “state” when evaluating the file one at a time), and then you can define your circle nodes in this “state” before switching to your rectangles.
Depending on your platform, you can also import your .dot file and configure it to publish. There are also a large number of generators and converters for the format.
Remember that if you are working on Mac OS X 10.7 “Lion”, I have not yet been able to find or create a working version of Graphviz. In this case, I would say that it is not yet suitable for your needs.
Art taylor
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