Viewing the website structure in this way can really help to spot problems. For example, while working on the new app I spotted a couple of pages on one of my sites that seemed to have more internal links than others in their level. Turns out those two have out-of-date navigation menus.
Look out for SiteViz, work is progressing well. If you have any thoughts about website visualisations (or displaying .dot files generally) then I'd love to hear from you - either in the comments or any other way that suits you.