Much of the solution to this is straight forward. Methodologies should be clearly expressed in detail at the start of the paper; all studies should be publicly logged before they start (so it's not possible to hide studies which say the "wrong" thing); resources should be made available so factors such as randomisation can be properly understood and executed with little or no additional effort. The more information is available the more likely

I'd go on but Ben Goldacre has said it all far better than I could, and in far greater detail in his book Bad Science which I think has just been released in the US (http://www.amazon.com/Bad-Science-Quacks-Pharma-Flacks/dp/08...).

What is important though is not to assume that because the evidence for conventional medicine is sometimes weak, that that in some way makes the case for less mainstream alternatives.

Flaws in one do not in any way strengthen the other, and for alternative medicine the evidence and studies are almost always either even weaker or non-existent.