This website lists the current top 100 Drupal websites (with a few limitations).
Edit (2013-12-02): http://topdrops.org lists the top Drupal websites (in the top 1 million websites worldwide) and it updated weekly.
Where does the data come from
The top sites list comes from Alexa as sold by Amazon (which owns Alexa) through their Web Services.
Currently the site data is then gathered with a custom module that parses them in serial (needs to be rewritten to be faster with a non-blocking rolling cURL ripper some time in the future). The same module also obtains the detection JSON from the Wappalizer project and re-implements it as PHP logic on the fly.
I didn't write additional logic to try to determine if a site is using Drupal when the site takes obvious measures to obfuscate the use of Drupal. Many top-end sites prefer to keep such things hidden.
One large part of the detection logic of Wappalizer needs a JS run-time environment which is obviously not available to the PHP parser.
A Bit of History
The site was first put together to get a better idea of the top South African websites that run Drupal as we're in the beginnings of putting together Drupal Association South Africa. It ran a few times already to generate the top South African websites for us, the history of which is available here: http://top-sa-drupal-sites.burtronix.co.za
Other Drupal labors of love in "free" time like this podcast aggregator for Drupal http://drupal-podcasts.burtronix.co.za with a unified feed and "real work" will likely hold the ideas up a bit. But it would be great to pick a different country every month to generate statistics for in the near future. The ripper can do with better code and unifying the sites will be nice too. Finally, a new theme and exposure of more data, like a migration list over time to see which sites moved to and from Drupal. These items may well wait to serve as a great project to learn D8 with over December.