On review, I will admit my original point was framed somewhat imprecisely. I did not mean to imply that it is highly unlikely that the government can manage to keep any large projects secret. I meant (as I think was obvious from the context) that it is very unlikely that the government would be able to keep something as large-scale, civilian-intensive, public, and high-profile as faking a series of moon landings secret for four decades. This probability is particularly low considering the alternative of, "They just did it." As my original point was a rather offhand comment, I did not bother going into this level of detail.
Someone is being intransigent here.
I will confess to not really giving a damn about the details up to now, because I thought my point was rather obvious. I see there's a bit of an inferential gap. In short, I think you vastly underestimate the prior improbability of your own claim, and vastly overestimate the relevance of your counterexamples, all of which are substantially different on numerous dimensions. I'll spell things out in greater detail.
[Having taken two minutes to look at wikipedia, there does seem to be rather solid evidence of its veracity, what with the fact that there is experimentally observable apparatus on the moon where Uncle Sam says we landed. That's besides my point, since it was strictly on the implications of massive government conspiracies being unlikely.]
There are pretty much exactly two possibilities: (1) the events are true as they were told to us, or (2) there was an elaborate conspiracy involving, on the one hand, whoever faked the actual video, and, on the other hand, whoever built all of the equipment to fake the launch, and every single significant person involved to this date has remained dead-silent. Other evidence is of course relevant to the ultimate question, but I'm sticking to my specific claim.
It seems fair to assume that if the moon landing were not technically feasible, some reputable scientist would be able to point this out. Therefore, if it is technically feasible, the simpler explanation is that things happened as claimed - what's the benefit of faking it, and burning enough money to actually do it, when you could just actually do it? The conspiracy theory requires, in addition to a massive, complex conspiracy, the total silence of people who would likely have realized the equipment they were making would not work, or who were not actually making equipment.
People wouldn't be driven to blow the whistle due to moral concerns - they'd be driven to do so for pure self interest. They'd become rich and famous if they had credible evidence. This is absolutely not the case for any other conspiracy you have named. That is an enormous distinguishing fact that you haven't appreciated. None of the examples you gave were such that people stood to become rich or famous by blowing the whistle. And the Cold War is over, and still no one came forward, so patriotism is a pretty unlikely explanation.
More importantly, every single one of the counterexamples you've given is a non-story. It's a lot easier to convince my spouse I'm not cheating by saying nothing than it is to do so by explaining on how I went on a luxurious tour across South East Asia, complete with video and tchotchkes. In every example you cite, it isn't that the government told us a story that happened, and that then got proven wrong. It's that the government didn't tell us there was a story, and then people figured out there was. (And how long did "Nuclear testing is perfectly harmless" last in practice?) There was no serious public question of, "Is the government honestly studying syphilis, or is something else going on?"
Getting the government to run a conspiracy of this magnitude with no credible leaks of any kind, despite massive personal incentives to leak, requires a whole lot of things to go exactly right. Actually landing on the moon, after developing a robust space program and spending enough money to develop landing on the moon and launching giant rockets into space and having videos of people landing on the moon, is not nearly so unlikely.
Date: September 11th, 2001.
Personnel: Unknown [designate A], Unknown [designate B], Unknown [designate C].
A: It's done. The plane targeted at Congress was crashed by those on-board, but the Pentagon and Trade Center attacks occurred just as scheduled.
B: Congress seems sufficiently angry in any case. I don't think the further steps of the plan will meet with any opposition. We should gain the governmental powers we need, and the stock market should move as expected.
A: Good. Have you prepared the conspiracy theorists to accuse us?
B: Yes. All is in readiness. The first accusations will fly within the hour.
C: Er...
A: What is it?
C: Sorry, I know I'm a bit new to this sort of thing, but why are we sponsoring conspiracy theorists? Aren't they our arch-nemeses, tenaciously hunting down and exposing our lies?
A: No, my young apprentice, just the opposite. As soon as you pull off a conspiracy, the first thing you do is start a conspiracy theory about it. Day one.
C: What? We want to be accused of deliberately ignoring intelligence and assassinating that one agent who tried to forward specific information -
A: No, of course not! What you do in a case like this is start an accusation so ridiculous that nobody else wants to be associated with the accusers. You create a low-prestige conspiracy theory and staff it with as many vocal lunatics as you can. That way no one wants to be seen as affiliating with the conspiracy theorists by making a similar accusation.
C: That works? I know I'm not the brightest fish in the barrel - sometimes, hanging around you guys, I feel almost as dumb as I pretend to be - but even I know that "The world's stupidest man may say the sun is shining, but that doesn't make it dark out."
B: Works like a charm, in my experience. Like that business with the Section Magenta aircraft. All you need is a bunch of lunatics screaming about aliens and no one respectable will dream of reporting a "flying saucer" after that.
C: So what did you plan for the 9/11 cover conspiracy theory, by the way? Are the conspiracy theorists going to say the Jews were behind it? Can't get much lower-prestige than anti-Semitism!
B: You've got the right general idea, but you're not thinking creatively enough. Israel does have a clear motive here - even though they weren't in fact behind it - and if the conspiracy theorists cast a wide enough net, they're bound to turn up a handful of facts that seem to support their theory. The public doesn't understand how to discount that sort of "evidence", though, so they might actually be convinced.
C: So... the Illuminati planned the whole operation?
B: You know, for someone who reads as much science fiction as you do, you sure don't think outside the box.
C: ...okay, seriously, man. I don't see how a theory could get any more ridiculous than that and still acquire followers.
(A and B crack up laughing.)
B: Hah! What would you have done to cover up the Section Magenta aircraft, I wonder? Blamed it on Russia? To this day there are still people on the lookout for hidden aliens who overfly populated areas in gigantic non-nanotechnological aircraft with their lights on.
A: So what did we pick for the 9/11 cover conspiracy, by the way?
B: Hm? Oh, the World Trade Center wasn't brought down by planes crashing into it. It was pre-planted explosives.
C: You're kidding me.
B: Seriously, that's the cover conspiracy.
C: There are videos already on the Internet of the planes flying into the World Trade Center. It was on live television. There are thousands of witnesses on the ground who saw it with their own eyes -
B: Right, but the conspiracy theory is, the planes wouldn't have done it on their own - it took pre-planted explosives too.
C: No one is going to buy that. I don't care who you bought out in the conspiracy-theoretic community. This attack would've had the same political effect whether the buildings came down entirely or just the top floors burned. It's not like we spent a lot of time worrying about at what angle the planes would hit the building. The whole point was to keep our hands clean! That's why the al Qaeda plot was such a godsend compared to the original anthrax plan. All we had to do was let it happen. Once we arranged for the attack to go through, we were done, we had no conceivable motive to risk exposure by planting explosives on top of that -
B: Don't take this the wrong way. But one, you don't understand conspiracy theorists at all. Two, they bought the aliens, didn't they? And three, it's already online and the usual crowd of anti-establishment types are already snapping it up.
C: Are you joking?
B: Honest to Betsy. People are claiming that the buildings fell too quickly and that the video showed ejecta corresponding to controlled demolitions.
C: Wow. I don't suppose we actually planted some explosives, just to make sure that -
A: Oh, hell no, son. That sort of thing is never necessary. They'll turn up what looks to them like evidence. They always do.
C: Aren't they going to, um, suspect they're pawns?
A: Human nature 101. Once they've staked their identity on being part of the defiant elect who know the Hidden Truth, there's no way it'll occur to them that they're our catspaws.
B: One reason our fine fraternity has controlled the world for hundreds of years is that we've managed to make "conspiracy theories" look stupid. You know how often you've ever heard someone suggest that possibility? None. You know why? Because it would be a conspiracy theory.
A: Not to mention that the story would be too recursive to catch on. To conceal the truth, one need only make the reality complicated enough to exceed the stack depth of the average newspaper reader.
B: And I've saved the dessert for last.
C: Really?
B: Yeah. You can go totally overboard with these guys. They never notice and they never suspect they're being used.
C: Hit me.
B: We've arranged for them to be called "truthers".
I hereby dub any believers in this theory 9/11 meta-truthers.
I, Eliezer Yudkowsky, do now publicly announce that I am not planning to commit suicide, at any time ever, but particularly not in the next couple of weeks; and moreover, I don't take this possibility seriously myself at the moment, so you would merely be drawing attention to yourselves by assassinating me. However, I also hereby vow that if the Singularity Institute happens to receive donations from any sources totaling at least $3M in 2010, I will take down this post and never publicly speak of the subject again; and if anyone asks, I'll tell them honestly that it was probably a coincidence.