OK, I am after all a reality based candidate, and not only that but will openly discuss reality without hesitation or apology, and am thus some fair distance outside the political and media mainstream. So let's just get this out of the way ...

The Communist Conspiracy:
This one's clearly past it's heyday, but reading about it I've never been able to figure out how communists were supposed to insidiously take over a country that was supposed to universally abhor them.

The Kennedy Assassination:
There's room to speculate otherwise, but my guess is it was a lone gunman in a fateful spot with some lucky shots. Maybe not, but probably.

The Freemasons:
My cousin's a Freemason, and I'm confident he isn't in on any conspiracy. Of course, maybe they just haven't told him about it. I probably wouldn't. And I can understand the desire for some kind of hidden explanation for grown men driving around in go-carts wearing fezzes. A lot of people aren't entirely comfortable with that.
addendum: It's been pointed out I may be confusing the Freemasons with the Shriners here. Shows what I know. If so, apologies to both organizations.
addendum2: OK, I'm now given to understand that the Shriners are sort of the the armed go-cart wing of the Freemasons. Maybe if they weren't all so shadowy this would be clearer.

Skull and Bones:
Freaky stuff in colleges! Who knew?

The gays are going to take over:
I'm just plain tired of hearing about this one.

The Gold Standard:
I think this one involves Nixon, so admittedly there's a conspiratorial aspect to it, but however the gold standard worked exactly I don't think it was a dark hidden conspiracy that got us off of it. More likely it was just the rich getting richer.

Fluoride in the water:
OK, I'm actually in on this particular conspiracy, but if I talk ..... well, you know what will happen. But I can tell you that it definitely doesn't involve the dentists.

UFOs:
I just don't think so. I expect any species that could cross intergalactic space could stay completely out of the Enquirer. Of course, maybe they don't want to. Hm. .... Hm.

The Federal Reserve Board is up to something:
Let's face it- almost no one has any real idea how the monetary system actually works, but if there is indeed a vast conspiracy surrounding it, whatever the point of it is I at least am in no position to complain. And let me just add that I don't see where it makes any real difference how much gold may or may not be sitting in Fort Knox.

The federal income tax is unconstitutional:
The sixteenth amendment to the Constitution may not have been the brightest bit of Constitutional amending we ever engaged in, and I always wonder what people thought the government was supposed to need all that money for if there wasn't going to be a corresponding amendment opening up a commensurate money pit, but how a Constitutional amendment could be unconstitutional is beyond me.

The CIA killed Janis Joplin, Jim Morrison, Jimmy Hendrix, etc,:
And every other person addicted to alcohol or drugs.

There's a conspiracy to bog the US down in an open ended land war in the middle of Arabia:
Like that'll ever happen.

There's a secret device that will let your car run on water, but the big oil companies have it locked away:
No they don't. And don't make me write out the equations.

Politics is controlled by a ruling elite:
Not on this website.

The moon landings were faked:
I worked at NASA for a number of years, so I can understand this belief. But I always like to pose the question of where reality ends and the conspiracy begins- we know people fly, we know there are rockets, there seems general agreement people go into space, if you can get into space the moon is a kick away, if you can get to the moon it seems you could land there, etc. The physics is somewhat daunting in application but straightforward enough on paper. Besides which, faking a moon landing and keeping it secret would be harder than actually doing it, though I will admit that under the threat of a funding cut NASA would probably fake a mass suicide for the insurance money if they had to.

Armageddon:
I was recently explaining to someone how the endtimers must be a declining group, since they're bound to increasingly notice that all the other endtimers throughout history have been proven wrong by the world's continued existence, but then I realized the flaw in my logic. Unfortunately, the only difference between the current endtimers and all their billions of predecessors is that the latest batch may for the first time have one of their number in a position to more or less pull the thing off. I'm not entirely sure why all the non endtimers aren't frantic about this.

The Illuminati:
OK, let me just go look this up .... dictionary's not showing anything particularly sinister, will try Wikipedia ... swear to god, front and center is today's featured article on The Illuminatus Trilogy. Quite a coincidence .... or is it? "The trilogy is a satirical, postmodern, science fiction-influenced adventure story; a ... trek through a number of conspiracy theories" Well ... I'm just going to read about the Illuminati and make a satirical remark about them anyway ... Wikipedia says they're "an alleged shadowy conspiratorial organization that controls world affairs behind the scenes". Yeah, well, I think anybody who thinks the world is under some sort of illuminated all encompassing control hasn't been paying attention. No matter what unlikely coincidences I encounter. Because they're just coincidences.


Things that aren't conspiracy theories:

The American/Israeli Public Affairs Committee isn't a conspiracy theory, it's the most powerful lobby in the United States. The neocons aren't a conspiracy theory, they're a small group of political insiders substantially driving US foreign policy. Israel isn't a conspiracy theory, it's a religiously based European nation in the Middle East with a population the size of Houston and hundreds of nuclear warheads.

The military-industrial complex isn't a conspiracy theory, it's a ... well, a massive military-industrial complex.

The Bureau of Alcohol, Tobacco, and Firearms killing people for no really good reason isn't a conspiracy theory, and if it hasn't happened lately it isn't because they shortened their own leash.

Implantable radio frequency tracking, 24/7 surveillance, personal monitoring on a scale and to a degree Stalin or Orwell couldn't imagine- these things are not a conspiracy theory but a very real and widening possibility, and make no mistake but that the only limitation is what people will tolerate.

The increasing lack of verifiable voting isn't a conspiracy theory, it's a fact.

The imminent possibility of genetically engineered viruses of sufficient lethality and transmissibility to eradicate humanity isn't a conspiracy theory, it's a looming reality, and waiting until it gets here to deal with it is not a sound option.

The existence of thousands of nuclear warheads, each of which can destroy an entire city and irradiate the surrounding countryside, isn't a conspiracy theory, any more than the extraordinary expenditure of money necessary to bring this possibility about.

And speaking of conspiracy theories, check out the roll call at the Project for the New American Century.