Another one nobody really talks about is the whole "UFO coverup conspiracy" which isn't a conspiracy to cover up UFOs, but to hide military operations:
The classic case, well-known to conspiracy aficionados, is Paul Bennewitz, a successful electronics entrepreneur in New Mexico. In 1979, Bennewitz started seeing strange lights in the sky, and picking up weird transmissions on his amateur equipment. The fact that he lived just across the road from Kirtland air force base should have set alarm bells ringing, but Bennewitz was convinced these phenomena were of extraterrestrial origin. Being a good patriot, he contacted the Air Force, who realised that, far from eavesdropping on ET, Bennewitz was inadvertently eavesdropping on them.
Instead of making him stop, though, Doty and other officers told Bennewitz they were interested in his findings. That encouraged Bennewitz to dig deeper. Within a few years, he was interpreting alien languages, spotting crashed alien craft in the hills from his plane (he was an amateur pilot), and sounding the alert for a full-scale invasion. All the time, the investigators were surveilling him surveilling them. They gave Bennewitz computer software that "interpreted" the signals, and even dumped fake props for him to discover. The mania took over Bennewitz's life. In 1988, his family checked him into a psychiatric facility.
Paul Bennewitz died in that facility, still paranoid. Our government broke that man, a veteran, with a conspiracy.
It makes it hard for me to enjoy the X Files knowing all the suffering caused by its origin.