I like PubPeer, which has a nice firefox extension and is well integrated with pubmed's comments system. It seems to have an active community, and some anonymous person is going through a lot of papers published in high impact journals and highlighting possible artifacts.
AcaWiki is like a "Wikipedia for academic research" designed to increase the impact of scholars, students, and bloggers by enabling them to share summaries and discuss academic papers online
Google side wiki ? http://www.google.com/sidewiki/intl/en/index.html
and the ooooooold Annotea http://www.w3.org/2001/Annotea (only works for GET urls...)
Alternatively, you can blog about the article. Websites like ResearchBlogging, Chemical blogspace and NatureBlogs, and the PLoS journals will index those blogs and link the comments to the papers. Using userscripts you can have those comments show up on the journal website when you use your GreaseMonkey-enabled browser (e.g. Firefox or Chrome) to look at the article website (see doi:10.1186/1471-2105-8-487).
An example screenshot of a journal ToC:
All of the BioMed Central journals accept comments on journal articles, so that is currently 207 journals.
They have a policy on comments which you can access here :-
I've had this site going for several years but update only on occasion. It's a pet project with no users but it has some legs.
Registration is disabled right now, so don't try. I'll update this post or reply when it's up.
It has some more work to go but I hope to push it to git in a week or two.