I can't find any recent numbers on HTML usage, but this site has some figures from 2 years ago.
Here's a small-scale poll of web developers (figures will be skewed since it's from a development site) from 2008 as well.
But it's probably best to just choose your HTML version or doctype by looking at browser support. On new projects, you should just use the latest version of HTML/XHTML that is well-supported across all browsers.
Possible answer, I will only select my answer as the correct one if up voted 3 times:
Also, found these of interest too: