Discussion forums built around academic journal articles haven’t seen much usage from readers. Lessons learned from the behavior of sports fans may provide some insight into the reasons why.
The scientific discussions that many researchers have found the most productive are often those sitting around a table in a informal setting, like a pub. These discussions are often wide-ranging and very open. They often produce really innovative ideas, which get replicated on cocktail napkins.
Some of the best ideas in scientific history can be found on such paper napkins. Simply allowing comments on a paper does not in any way replicate this sort of social interaction. But there already online approaches that do. We call them blogs.
Check out the scientific discussions at RealClimate, ResearchBlogging or even Pharyngula. Often the scientific discussions replicate what is seen in real life, with lots of open discussion about relevant scientific information.
If journals want to create participatory regions in their sites, they might do well to mimic these sorts of approaches. David Croty at Cold Spring Harbor has such a site. Although it has not reached the popularity of RealClimate, it is a nice beginning.
I would think that research associations, with an already large audience of members, would have an easier time creating such a blog, one that starts by discussing specific papers but is open to a wide ranging, semi-directed conversation.