I consider most of them to be jokes taken too far on people with no sense of humor. Once in a while though, a theory comes along that actually has factual information that might not prove the theory, but completely obliterates the accepted "fact"; two of them were already mentioned - JFK and 9/11. It's pretty much common sense to look at the official reports and say, "Phhh! Are you kidding me? One person firing that often with every bullet twisting and turning in mid-air to hit that many targets? What the hell are you smoking??" but what the actual truth is, is still a mystery.
What feed the fire in most of these cases is that no one every officially comes out and says, "Hey, you know that report we released? Yeah... um... we screwed up. We meant there were actually 2 gunmen." It's just easier to let the people with some degree of common sense and intelligence look at the facts, argue against the reports and come out looking like the tin-foil hat crowd.
Then again, now and then, decades after the fact, when most of the people are dead or incapacitated, you hear of plots and conspiracies that are actually true.
The Business Plot, which was proven to be true about 25 years after the fact for instance... and comes eerily close to the government we have today.