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.
Not just logged, but accepted by journals. I.e., you submit a paper, explain the experiment design, and put in dummy tables. The conclusion section is unwritten.
The journal accepts or rejects based solely on methodology - they can't reject you after the fact for going against conventional wisdom or getting a null result.