Unfortunately, it is currently very difficult to conduct a good controlled scientific experiment to study acupuncture and other alternative modalities and it might always will be. There is simply no good means by which to have a "control" group for an acupuncture treatment. This is frustrating, because the acupuncture naysayers are technically correct in this regard. It drives me crazy. As someone who was trained in Western sciences (I have a BA in biology and have worked in numerous university labs), I understand the dilemma and yet it still drives me crazy.
Despite this "shortcoming", I continue to believe acupuncture to be a valid science. There is simply too much empirical evidence that has been compounded over thousands of years and millions (billions?) of patients. It works.
Luckily, I am not alone - here's a really good article that articulates my position better than I can. Give it a read and see what you think.