One challenge I've found is that it's often difficult for discussion sites to gain sufficient traction to build a critical mass of discussion - http://plasmyd.com, http://papercritic.com, http://scicombinator.com, http://chemfeeds.com.
I wonder if focusing on supporting existing small-group interactions (real-life journal clubs) would help?
I took a slightly different approach when I wrote http://www.papernautapp.com and chose instead to aggregate existing discussions about academic papers (mostly blogs, a few news sites, HN, and r/science, with a goal to cover to more sites and mailing lists). It's also freely licensed, and there are some interesting things I discovered that might be useful to OpenJournal (looking at your TODO list and GH issues):
* CrossRef.org runs a ton of cool lookup/crossref/deref services at http://labs.crossref.org/
* They also have some great libraries at https://github.com/crossref/ - who wouldn't geek out at this: http://labs.crossref.org/pdfextract/
* If you want to do some auto-identification on webpages, the https://github.com/zotero/translators project is great and actively maintained by the Zotero community.
(Some notes on how Papernaut is put together, if you're interested: http://jayunit.net/2013/01/06/papernaut-exploring-online-dis... )
Lastly, if you're fostering discussion and feedback on papers, there's overlapping interest with the http://altmetrics.org and http://altmetric.com folks.