The different colors represent different aspects of the particular website...and of course the branches are based on algorithm information. I won't even pretend to understand that part!
My other blog looks like this .
Found this at Miss Rumphius Effect...you can see what that blog looks too!
P.S. These are screen shots...the only way I could figure out how to show them to you. You can also go to Flickr and use websitesasgraphs as the search term. Mine will be there...soon!