1. MK-ULTRA
The government of the USA has a LOT of secrets. We know that, and none of it is actually surprising. And, of course there are quite a few conspiracy theories involving them. The MK-ULTRA was actually a code name for one of their projects. They were doing experiments about the human behavior- read that as mind control. Yes, sir, they actually did this. And they involved the CIA in it too.
This particular program began in the early 1950's, and it was officially stopped in 1973. They used involuntary people in it, by administering drugs to them (especially LSD), and also some crazy chemicals. They tried hypnosis on them, sensory deprivation, isolation, verbal and sexual abuse and a bunch of other torture.
They had 80 institutions of this kind, including 44 colleges and universities, hospitals, prisons and pharmaceutical companies.
Basically, they wanted a way to manipulate the mind and to extract information during interrogations.
2. Asbestos
We all know by now that asbestos causes many illnesses, starting with respiratory problems and ending with cancer. The funny part of it is that the manufacturers of asbestos also knew. Even back as far as 1930. American workers even sued one of the companies back in 1932, but they stuck to the fact that it was actually healthy. They managed to hold this up for another 30 years, until 1962.
3. Operation Northwoods
Do you think that there is no way that the USA would actually be behind terrorist attacks against their own country? You know, all that 9/11 crap. Well, here's a surprise for you then. It already happened once.
Back in the early 1960's they made plans to create a public support for war against Cuba. These plans included killing innocent people and soldiers, blowing up ships, assassinating people who emigrated from Cuba, sinking boats of Cuban refugees, and also - surprise, surprise, hijacking planes.
For 40 years these plans were kept under secret. Thankfully, the civilian leadership rejected it, even as the Joint Chief of Staff gave it a thumbs up.
Oh, by the way - if this raises some questions in you, you should also check out the Gulf of Tonkin conspiracy theory. Basically the same thing happened (as in, the US made up a story to escalate a war).
4. Operation Paperclip
This is one of my favorites, actually. It happened when the second World War was coming to an end. The Third Reich was going down, and people were fleeing the sinking ship like there was no tomorrow (and for some there probably wasn't).
Of course, the special forces of the USA realized that it would be a pity if intelligent people would lose their life in the craziness of that world. Especially, when they could be used for the "interest of the USA".
Thus, they smuggled into the country a big group of Nazi rocket scientists, medicine experts and let's not forget people from the chemical weapons division. There were actually about 700 of these people. So, yeah, ladies and gentlemen. Fascinating, eh?