Apologies for coming late on the scene, but I worked back in the day for a design firm known as Plumb Design who developed a tool called Thinkmap. You may recall the Visual Thesaurus project. Plumb is now known as Thinkmap and the software is available for sale on their website http://www.thinkmap.com
I'd never heard of the Tom Sawyer product but its range of examples is intriguing. Inxight, Thinkmap and it seems Tom Sawyer all use some similar core java libraries to create lines and nodes. As far as I'm aware, Flash will freeze up your processor trying to render a really dense data visualization, especially if there's animation of any kind. Joshua Davis of Praystation demonstrated this limit awhile ago with his motion widget studies. A counter example might be Josh On's They Rule project http://www.theyrule.net which performs well. I'm not advocating any particular solution, but you best do your homework on the various issues people have already on this thread - viz metaphor, parameters, biz process, etc.