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I "think" for now they are just scouring the web to find the best route to access various parts of the country or world. Like if there is a lag from point A to B to C to D then re-route the connection so that it goes from point A to E to F to D. This would explain them finding sites by IP address instead of DNS.
They might have some other uses for this in the future if they have not already implemented it. I could imagine someone like Inktomi using this to their advantage on their search engine database.
First they rank all the sites they spidered in terms of relevance, then rank them in terms of connectivity. Whoever has the best of both worlds gets a better listing. Or if a site is down too often then it gets dropped out of the index.
I agree. From reading through Inktomi's Traffic Server info page it looks like InterNap is a real influence on how their server functions.
Here is some info on them financially if you haven't already come across it.