The Disqus plugin for WordPress can sync comments to your database. That way you still have your comments if Disqus goes down, or you decide not to use it. I still go with native because I prefer the way it looks. :)
But what if the service goes down during the night time where I might not be able to immediately login to my wordpress and disable the Disqus plug-in until next morning?
Wouldn't be nice if the plug-in automatically takes care of itself, rather than manual intervention?