You need to put files like comment.html in your flavour directory, not your datadir (as the comment documentation on the pyblosxom site incorrectly states).

The nospam plugin (without AJAX) is not working for me. I see the captcha, and I enter it correctly, but it says it's invalid. I think it's an issue with the session plugin. I've given up on captchas for now. Hopefully I won't need them.

The mta configuration of the comments plugin was not working correctly. I'm supposed to get email whenever someone comments, but the plugin was set up to use mail arguments rather than sendmail arguments. It was also double quoting the subject line for some reason. I edited the comment plugin to make it work with sendmail. You can find that patch here.