I think the main one would be that, with JoComment, unregistered users can also comment. With a forum, they have to be a registered member of the site to comment.
On top of that, this commenting extension is very lightweight compared to a full-fledged forum. The article pages would be much quicker in loading time.
Something i'd like to have (and will look into making it possible) is a plugin for the article editor where, the author can add a link to a forum thread, and it will disable JoComment - instead placing a 'Comments are disabled - discuss in forums' with a link to the thread.
With that said, a comment system is best suited for publications of review or in-depth opinion; a forum is more of an open discussion platform and has the extra tools (and bulk) to accomodate for that. I plan to use both JoComment an Kuena on my site.