I was wondering the same thing. Turns out that he's using Analytk, a project that he created himself.
Here's what it appears to do:
1. A referrer information is gathered on each page hit via javascript and submitted to his server
2. The Analytics page uses Ajax to grab the aggregated data, then charts it using the Google Charts API
That's it. At first I was really interested in it because its beautiful, but on a second look it doesn't do anything that Google Analytics doesn't already do except easily show you referrals from a set of sites that you care about.
I wrote it because it gives me real time tracking for posts that have just been published. Initially it updates every minute, which is really fascinating to see. The rate of hits once the site is picked up by HN or Reddit is a very strong predictor of it's final page view count.
The graphs get a bit pointless after a day or two, though. If people are interested in playing around with analytk then maybe I'll open it up to URLs from elsewhere and work down some of my 'to do' features, like 'show me just the day/week'.
Thanks for the beauty vote, I wrote it to look great on my iPhone :-)