what about vitamin D? haven't there been eleventy billion studies that all say we don't get enough?
There probably have, but the layman (and even though I've read up on this a decent amount and have a healthy interest in the subject, I
have to still consider myself one) cannot disseminate the information from these studies, and we don't know the results of the studies that haven't been published.
Your best approach is a 'bayesian' one, infused with a healthy dose of common sense. We know that smoking is bad. Why? Well, apart from the sort of obvious idea that inhaling the result of burning stuff is going to be bad for you, we have 40 years of empirical and anecdotal evidence and only wackjobs claiming that it's not. It's got to the point where we can now say with some confidence that too much salt is bad for you, but even in this regard there's a lot of confusion. How much salt is too much? Could we do away with salt entirely?
There are three ingredients in food that are generally responsible for good flavour: salt, fat, and sugar. Too much of any of them is bad for you and the media have made sure you know it. The result is that food manufacturers (ready meals, chocolate bars, crisps, etc etc) often advertise their product based on one of those three things being reduced or entirely free from, but to make sure it tastes good, they usually bump the sh** out of the other two, meaning that many of the products you see on the shelves saying 'fat-free' or 'reduced salt' could be very, very unhealthy.
NoahSD is the nuts and he made a very good blog entry about this topic a while ago:
http://www.nsdpoker.com/2011/02/human_body/