I use PyBloxsom with the PyMarkdown plugin and I've been very happy. When I had to convert all of my posts out of MT into something else, PyMarkdown was very helpful with formatting, etc. I picked PyBloxsom over Wordpress and others because I realized that I really hated writing posts in a textarea form. I preferred to use my usual editor, and with Markdown, I can do simple formatting without any problem. (I would think this would be a huge plus when trying to post code, which Markdown handles very well.) I use PyBloxsom's static generation feature, so when I'm done editing, I just "build" the site and RSS, indices, etc. are all updated. (And if you do decide to make any changes, the code is compact and in python. And no database!)
If you really want threaded comments, or comments at all, I think it's better to outsource them to a company. Spam filtering is a huge pain, and gets worse the longer you have site. Let someone else handle it.
I've tried Textile, still use MoveableType for GB, and WordPress. They all drove me nuts. Using emacs and a couple of simple shell scripts didn't, and that's the best way forward I think.