After having mucked yesterday with my WordPress to add threading to my Atom feed, I found there’s a better way. I’ve taken James Snell’s Atom 1.0 templates, fixed them up a little bit, and packaged them as a WordPress plugin (instead of uploading them directly into the WordPress install, which makes it hard to upgrade WordPress). Installation instructions. Source code.
Update: James says his templates are public domain, and I am putting my changes and plugin glue into the public domain as well.