About a year ago, LyndaCarol suggested we have a forum on multiple sclerosis hypotheses. I guess that didn't happen but it seemed like autoimmune disease hypotheses would be a good topic for a journal to cover.
The journal, Clinical Reviews in Allergy & Immunology, has just published an issue (Feb. 2012) on hypotheses of autoimmune diseases, such as the hygiene hypothesis, leaky gut hypothesis, molecular mimicry, etc. I can't post the articles but you might take a look. http://www.springer.com/medicine/internal/journal/12016
I slipped in my polyamine hypothesis, which has evolved a lot since we discussed it on TIMS 8 years ago.