In a recent blog post, Kai complained about various existing tools for marking up email in HTML. He also asked for pointers to other tools. Since he didn't specify good tools :-), I took the opportunity to promote my work in progress plugin for ikiwiki to do that very thing.
When asked about demo sites, I realized that my blog doesn't actually use threaded comments, yet, so made a poor demo.
Follow the link and you will find one of the mailboxes from the distribution, mostly a few posts from one of the debian lists.
The basic idea is to use the Email::Thread perl module to get a forest of thread trees, and then walk those generating output.
I think it would be fairly easy to make a some kind of mutt-like index using the essentially same tree walking code. Not that I'm volunteering immediately mind you, I have to replys to comments on my blog working (which is the main place I use this plugin right now).