Cochrane (systematic) reviews regularly reject lots of studies they consider on the grounds of poor methods. For instance, here's a quote from a paper in the October 2000 issue of the Journal of Clinical Oncology: “From the 80 retrieved articles, 48 were rejected. All of these studies were of small sample size and many were also of doubtful quality.” 
A different perspective is provided by Richard Smith (former editor of the British Medical Journal):
“With medical research you can get anything published, there are so many journals and have been for a long time. Nobody knows exactly how many there are but there's probably something like 15 to 20,000 and you - to be honest you can get any rubbish published, you just go down and down and down and down the food chain, as we call it.” The Other Medicine Programme 2. BBC Radio 4 Tuesday 28/09/04
 From : Contribution of Dexamethasone to Control of Chemotherapy-Induced Nausea and Vomiting: A Meta-Analysis of Randomized Evidence Journal of Clinical Oncology , Vol. 18, Issue 19 (October), 2000: 3409-3422. Ioannidis, J. Hesketh, P. and Lau, J.