I don't think there's any way to really know this.

You can get some stats on downloads from a particular theme directory but that doesn't help much as:

a) there are so many places to get themes
b) themes that are downloaded aren't necessarily used
c) the default themes are probably very popular

Also the largest number of blogs are on Blogspot and Wordpress.com and many of them aren't even active any more. Quite a lot may have been created to play around with and quickly abandoned.

So by sheer number of blogs ever created, I'd guess Blogger's Minima or Wordpress's Kubrick themes are the most used.

http://lorelle.wordpress.com/2007/09/08/kubrick-and-k2-wordpress-themes-collection-of-theme-tips/

http://stopdesign.com/portfolio/web/blogger-templates.html

However, there's no way to prove or disprove the guess. :)

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