I'm a big fan of what the BMC series of journals and PubMed Central are trying to do. Nonethless, I'm not surprised if a few poor journals and/or articles in these journals show up. It is hard, if not impossible, to start a new journal and get only top notch science submitted to your journal. Bottom line is that these new electronic journals are probably hungry for submissions.
One good thing is that the online format allows for comments to be posted. I haven't seen much use of this; I think scientists aren't much into the idea of blogging or discussing papers in a public forum. Nonetheless, if anyone feels that they have legitimate problems with a paper, such as improper use of references, go ahead and post a question. I can't think of a more appropriate question to post to the authors.