What percentage of Stack Overflow users have over 10,000 rep?
On Stack Overflow, there are 5177 pages of registered users at 35 per page, but the last page isn't full, so somewhere around 181180 give or take a few hundred. There are 17 full pages of users with >10k reputation, and 3 more past that, so 598. 598/181180 gives a bit over 0.3%.
In simpler numbers, there are ~600 10k users and ~180000 users in total, which is around 0.3%.
You can also use this query I just wrote, showing count of users per reputation digits:
Summing the 5 and 6 digits rep users, there are currently 8825 users with 10k or more. (as of 6 hours ago to be accurate.)
This is only useful as a measure of active users, and there's no real way to determine that outside of being on the dev team. But we can use reputation to make a guess and filter out users who don't have at least 103 rep (100 rep bonus for cross-registering + downvote/upvote trick for new users). That returns about 1.5%
Refer to the "Total Reputation" table in the right sideboard about 1/4 of the way through the stackoverflow reputation leagues webpage. (Of course this resource was not available when the question was asked in early 2010; the leagues started a few months later, as noted in a 12 August 2010 blog entry.)
For the original question, "What % of stackoverflow users have over 10,000 rep?", as of 4 August 2012 it appears there are 2660 stackoverflow users with 10,000+ reputation, and 1,178,206 with 1+, giving a figure of 0.23%. (Versus the "~600 10k users and ~180000 users in total, which is around 0.3%" that GraceNote mentioned in May, 2010.) The 40005 users with 200+ reputation are 3.4% of all users. To see figures for other stackexchange sites, click the dropdown list at top of page. Also see some of the applications tagged reputation in stackapps.com.
Here's a SO Query to give you number of users with 10k reputation or more.
Click the Messages tab after running the query to view the total number.
As of this writing there are 8,823 users with 10k or more reputation.