I've been thinking about this for a long time.
Gamerz (from the WP forums) was talking about getting something like this working for phpbb a while back but his example link was broken, and nothing ever came of it.
Also, Matt, from WP developed bbPress, and writes a little in the dev list about how integrating the two should be easy to do.
imagine a WP post, and a bbPress series of responses? heavy...
As for punnbb:
My thoughts have been that it would be best to first create a uniformed look and feel.
either get punbb to look like your WP install
or your wordpress install to look like your bunbb design.
op ed:
(this is important for continuity... if you want to use one or the other as the "front end" of your site then it is essential. usually, in communities, when people find your message board, they just directly link there, and never read your pages or news sections again.)
once you have them looking very much the same, the easiest thing to do would be to disable comments on WordPres, and altar the "comments" link globally, and individually in WP.
modfy the link to either load the board inline below the post, or as a popup.
The tricky part is to get the number of replies between the two applications. but, punnbb has a superb rss addition that alexking (also a wordpress benefactor) developed.
possible you could maintain those counts on your main site with a feed.
i am not proficient in php to otherwise determine how you could hard code a function to go see how many replies there have been, and then output the number on the wordpress page.
(however, that code would end this issue, and solved the problem completely!)
dunnoe if my reply is even helpful...
good luck.