As another poster mentioned the Anthroprogenic Climate Change debate. There is still debate about it, and the more light that is shown into the data, data gathering and processing methods of the primary investigators the more questions there are. Other statisticians and researchers have had to use FOIA (and the British equivalent) to get "raw" data and other information from researchers. If you won't release your raw data, and you won't release methods for processing that data then you really can't agree on anything, now can you?

So-called Alternative and Complementary "Medicine" being taken seriously by journals and organisations who should know better. And this is when the good studies show very, very little real effect these frauds. Especially things like Acupuncture and (for things like pneumonia and cancer) chiropractic care (I will note that spinal adjustments can be very valuable for some spinal problems).

Meaning stuff like this: http://www.sciencebasedmedicine.org/?p=9912 (note that one of the main complaints of the author of that post is not that Chinese Medicine calls stuff by different (and humorous) names, but rather how it classifies and recommends treatment. This is a MAJOR point).

I also know people who've worked inside NASA and other labs and I know how much worldview and localized politics have influenced what got funded, and what was done with the funding. Not enough of the story to recount with any accuracy, but enough to know that there was a hand on the scales as it were.

I have a Popperish view of science, and I'm perfectly willing to accept that humans have some influence on temperature, I'm willing to buy that chemicals compounded by nature have greater effectiveness (or equal effectiveness with few undesirable effects) than chemicals compounded in a laboratory, but science is never settled, and if you want to hide your work you really don't deserve benefit of the doubt.