It hits the press from time to time that somebody was successful taking down a botnet. We had some success as well with the Waledac Botnet Takedown.
There is actually a good article on What it takes to shut down a botnet. When I was doing some bing-search on the botnet takedowns, I found good work from Microsoft research as well: Your botnet is my botnet: analysis of a botnet takeover.
It is not only about taking down the botnet, it is about going after the criminals and making sure it does not recover.