Wikipedia mentioned Roosevelt knowing about Pearl Harbor. I find that one pretty plausible. In a similar vein, while I don't think the Bush administration made anything happen, I suspect they were more negligent in the face of the attacks than they let on.
AIDs. There are a lot of crazy things people think about AIDs, but I'll give these conspiracy theories some credit. Most conspiracy theories exist in the presence of a perfectly satisfying and far simpler explanation. The thing is with AIDs is that it's emergence is still very mysterious, and the current assumption about it are confusing. Why did it infect the whole world almost at once if it's some central African mutation of shit endemic to apes? Why is it so different from that nearest relative? Why, after being in these creatures and even people all this time, did this HIV suddenly become AIDs in the 20th century? Why is it that the trend of the epidemic actually started mostly with North Americans and then Europeans, seriously breaking out in Africa virtually last? These things beg some explanations, so many theories are going to be formulated. I do have to wonder if human intervention is involved in the emergence of AIDs, though I don't imagine anything malicious so much as incompetent.