Yes, homepages and all the content subsequently loaded (directly or indirectly through multiple layers of scripting or iframes). Essentially what you'd get if you were to visit each and every homepage on the top list and logged the urls that were loaded as a consequence of that.
As much as I hate Flash, I don't think you can infer that then. Does your analytics consider https://www.youtube.com/ using Flash? I see no Flash on it here.
If it's not on the homepage then it would not consider it using flash. The analysis was run on the homepages, not on all the pages in those websites. (And that would require a lot more work on my part and likely would not change the results all that much).
I believe overall flash usage on the web is now about 10%, but larger sites are generally much better at keeping their sites up-to-date and to follow trends.
Advertising is another good indicator. The typical trick nowadays is to check if flash is installed using some javascript or header inspection and only to serve it up if support has been detected.
Websites that categorically include flash are the ones that were detected.
That's a good point though, I should update the text to that effect.
edit: ok, updated the text to be much more precise about flash usage and the conditions of the crawl which will lead to under-representation of flash.
