Right folks, I thought this process would turn out to be simpler than it actually is (this is the internet after all, and nothing is as simple as promised, but that's why we love it so. Right?)
As comment frequency has increased (a very happy thing!) I've become very dissatisfied with the default comments system, and others have reported problems with it as well (especially when they write long, thoughtful rebuttals to insane Doctor Who theories).
So I've moved to Disqus comments, which allows replies to be nested (amazing!), and you can subscribe to replies to your comment instead of to the whole thread (woohoo!).
But, Disqus is having problems importing old comments. Don't worry, they haven't been deleted, but it may be some time before I can restore them.
I hope this facilitates greater conversation moving forward!