Comment threading is enabled now, so you can now reply to a specific comment on a post and have it appear below it and indented — just like on LiveJournal or WordPress.com. See the comments on this post for an example.
The downside is that it required some changes to the theme, some of which I missed initially. If you’ve visited the site in the last few days, you may have seen some comments showing up in unreadable light yellow-on-white. That should be taken care of now, but if you still see it, just hit reload and it should be fine.
Technical note: It was a caching issue. New visitors, or anyone who hit reload, would get the updated stylesheet, but anyone who had visited the site recently would see it displayed with their local copy of the old version. After I realized this, I renamed the stylesheet to make sure that all visitors would get a fresh copy.