Summary: Current peer review is not 100%; we need to think in terms of authors' motivations (tenure); try a hacker news model, possibly layered with badges-of-approval from editorial board.
The quality of peer review is only as good as the editorial board and reviewers make it -- often this is a lower standard than we expect. This article lists several extreme examples of poor practices by a (previously-)prominent publisher:
http://blog.mathunion.org/journals/?no_cache=1&tx_t3blog...
The key to shifting academic quality control away from the present archaic model is through author's motivation. The replacement needs to be a system that improves and filters incoming papers, and at the same time earns at least as much prestige for the authors who participate.
One idea is something like a combination hacker news and stackoverflow with academic articles in place of news articles / technical questions as the object of discussion. Papers can be changed in response to comments. High scores for either a paper or an author on such a site could replace the prestige granted by acceptance into a top-tier journal. Points are awarded for reviews, and researchers are respected for their scores (closer to tenure), so there is more positive motivation to review than in today's system (which is: it's rude not to review when asked).
I think that alone could work. Some academics might balk at a lack of editorial boards. Fine, let's allow some editors in the mix. An editorial board is an aggregator. They choose what content fits their filter, and may open a discussion with an author on improvements, possibly bringing in reviewers. In the end, readers will see a prestigious badge of the board's approval on high-quality articles, and there could be a page or rss feed to browse the articles meeting this standard. This can all exist on top of the hacker news / stackoverflow system, which itself could be built on top of an arXiv-like system.
Several of these ideas are motivated by thoughts from the blogs of Tim Gowers and Michael Nielsen.