Heres some more stuff that was figured out from the website
1) The wesite
http://thepurification.org/ has several countdown timers on it.
2) The first online mention of the site seems to have been at stumbleupon.com on Sept 30. The person posting it got it from a friend and claims to be unrelated.
3) The last timer reaches zero on Nov 15th, 2006 at midnight EST.
4) There is an odd symbol in the center of the page - A circle inside a diamond inside a square.
5) There are four phrases revealed as the timers get to zero. These phrases seem to relate to restoring innocence, overcoming materialism, and purification/truth.
6) No obvious connection has been found between the phrases and things like Hopi myth, Scientology, various plays and movies, video games, TV, etc.
7) There are four towns revealed as the timers get to zero. Bitter Springs, AZ, Woodward, OK, Lookout, WY, Fort Hancock, TX.
8) Plotting the four towns on a map shows they are in a diamond shape similar to the symbol. Also, the towns are on the map in the same placement as on the website.
9) Nothing at the center of the plotted towns seems related.
10) Decompiling the Flash from the site shows no events taking place once the counters all reach zero. Also, no apparent clues are revealed in the Flash source.
11) The variable for the last counter in the Flash file is "countertaos". And the city of Taos is near the center of the plotted towns.
12) The site hosting is an ISP in Spain - cdmon.com
13) The domain registration points to a man who claims to know nothing about the site.
14) The GoDaddy account that registered the domain used an email from McKee Wallwork Cleveland - A marketing agency.
15) The font used in the site is Trade Gothic Bold Condensed, a popular commercial font among designers.
16) For a brief time a few days after the online hunt started a message showed up in the html comments for the site - "We see you. We know you're watching." in English, French, Spanish, and Portuguese