I've been using Disqus for a while now, as have others, notably AndyC.
There is a Habari plugin, but I'd strongly recommend not using it (it
was written before they had an API and is really hacky and buggy).
They have instructions for integrating directly in your theme.
I wouldn't outsource my comments again, and will migrate back to
native comments when I have the time to do so (which will probably
involve fixing the plugin and including comment export). Part of the
original attraction for me was outsourcing spam filtering, but I think
they've done a fairly poor job of managing spam. There are other
annoying things, like ending up with multiple comment threads for one
post (if a query string is different it will be treated as a different
post) and there's no way to tell Disqus they're the same post.
--
Michael C. Harris, School of CS&IT, RMIT University
http://twofishcreative.com/michael/blog
IRC: michaeltwofish #habari
There are quite a few comment outsourcing platforms. They each have
their own issues, and Disqus is among the best of them. Notable ones
include JS-Kit, IntenseDebate, SezWho (did that die?)