Does the President of the U.S. have absolute security clearance? For example, assume that all the Area 51 conspiracies are true, and President Such-and-Such wants the grand tour. Or President Such-and-Such wants to know who shot Kennedy…does the President get the Straight Dope??
I don’t believe so. I think, in addition to your security clearance level (even his), you’d need to demonstrate the classic “need to know.” Maybe he needs to know, maybe he doesn’t. But I doubt they’d let him see anything he wanted. Hell, Ike, the beloved military hero, had a bitch of a time just learning from his generals what the US’s plan was for responding to a Soviet nuke attack (and was apparently surprised to learn it meant killing half of the Northern Hemisphere, no questions asked).
And, of course, there’s never really a way for the Pres. to KNOW that he’s being told everything …
PRES: Do we have alien bodies in Area 51?
GENERAL: Ummm… no.
PRES: Okey-dokey!
As long as we’re reduced to mere belief, let me just say that “I believe.”
I believe that the President can see absolutely anything he wants. Period.
Whether he might need to specifically ask for an item, rather than being spontaneously shown the item; whether the military, CIA, NSA, or CNN will lie to him; whether he gets all the data he needs are all besides the OP.
If the President asks, that makes it “need to know.”
Can you refute this? 
What’s your clearance?
True, but that’s the more intriguing question. 
Yer a smart-ass, Cervaise!
AS best I can say from my one-time pigeon-eye level of security (Top Secret-Diplomatic with escort privileges for USAID and Dept of State) and the lectures we had to attend every few months I’d be willing to bet the President has access to anything he wants. He might get the classic ‘Sir, do you really want to know?’ question but he wouldn’t be denied.
I can just see it…
President: “Give me everything we have on Area 51 and those damn aliens.”
Intel Weenie: “Sir, I can’t give that to you. You’re not cleared for it.”
President (to secret service): “Arrest that man. He’s fired. Bring me his replacement and I’ll ask him to get me the stuff.”
Having the ability to (literally) destroy anyone in the federal service is a fine motivating factor.
Within reason, though. The Prez can’t casually sift through medical records, even of government employees, without a court order.
At least, I don’t believe he can.
And pace Nixon, he can’t go through their tax forms either. But that’s also not what the OP was asking.
Another roadblock for the president’s curiousity — we have three branches of government. The Congress and the Judicial Branch (Supreme Court, Federal Courts, U.S. Courts) are not obligated to share their confidential documents with the president or anyone else in the executive branch.
QUOTE:
“By tradition and practice, United States officials who hold positions prescribed by the Constitution of the United States are deemed to meet the standards of trustworthiness for eligibility for access to classified information. Therefore, the President, the Vice President, Members of Congress, Supreme Court Justices, and other federal judges appointed by the President and confirmed by the Senate need not execute the SF 312 as a condition of access to classified information.”
http://www.fas.org/sgp/isoo/sf312.html
Realistically, the whole national security apparatus is designed to deliver reliable information to the President and his advisors. How he interprets it and how he chooses to act on are different issues. Any lower level official who tried to conceal information from the President would be assumed to be pursuing his own agenda to the detriment of the country.
I can’t find a cite at the moment, but I have read that one of the most sobering experiences in a new president’s life is when he is shown how many millions of people would be killed in various nuclear war scenarios, and then is handed the card that lets him access the launch codes.
Also, the scrutiny that a presidential candidate gets during a multi-year campaign is vastly more exhaustive than an FBI background check. Who do you think is more likely to turn up dirt: a busy FBI agent calling your employers and checking your credit records, or armies of reporters and political opponents reviewing every moment of your life, starting with how your parents met?
Because a U.S. President can only serve a maximum of ten years in office (and usually just 4-8), it seems that some things might be kept from the CinC on the need-to-know grounds, but I’m only guessing.
By whom and for what purpose?
Slightly tangental, but IIRC on of the first things Clinton did when he took office was ask for all the poop on the Kennedy assassination.
Well, the Masters of the Illuminati, for one. What, you need a score card?
My impression is that while the various Presidents could ask for just about anything, they generally did not. In practice, they don’t ask because they generally don’t need to know. What they are after is what the facts are and how reliable those facts are; the details are left to the actual intelligence people.
For instance, the President might want to know how many SS-XX missiles are aimed at the US. They might even ask how reliable that estimate is. If told 100%, they might ask how we’re so sure and get the reply that an agent who is a very senior member of the Russian military is our source. But it would be completely unnecessary for the President then to ask what the agent’s name is, what their code name is, where and how they pass their information, what kind of car they have, what their spouse’s name is, etc. Practically speaking, the President wouldn’t care. (Unless the President were a spy for the other side or something.)
In real life, there was an agent whose code name was “Solo”. Solo had access to the highest levels of the Politburo on a regular basis (at least through the 1960’s, providing much very valueable information) and had been developed by the FBI (not the CIA). Solo’s identity was never shared with the President(s), and the President(s) never asked.
You beat me to it.
Among the traditional items that are specifically withheld from the President are names and identifying details of sources who are still in situ. One example would be a colonel in the Polish General Staff who had access to considerable information about Soviet and Warsaw Pact forces and plans in the late 70s and (IIRC) the early 80s. Every detail of his identity, or even the existence of an inside leak, had to be kept secret, lest a crackdown ensue.
President Carter has mentioned this specific exclusion in more than one interview. Bob Woodward (of Watergate fame) mentioned it in Veil: The Secret Wars of the CIA 1981-1987 [You may be able to find the specific story of the Polish colonel online. The Washingtom Post excepted it in: Woodward, Bob, and Michael Dobbs. “CIA Had Secret Agent on Polish General Staff.” Washington Post, 4 Jun. 1986, A1.]
Woodward’s book also details some of the internal politics of the CIA. Career staff are actually rather suspicious of the President and the DCI [Director of Central Intelligence], viewing them as “temporary” and “political appointees”. The DDCIs [Deputy Directors of Central Intelligence] for Operations and Intelligence, the second-in-commands of covert actions and analysis, respectively, both generally career CIA, often do most of the heavy lifting in running the Agency. The DCI oversees the actions of all 13 agencies in the US intelligence community, and writes all their budgets.
As to "who would tell the President “No”, I doubt it would come to that. The President generally deals in summaries, not full files, so he is generally not given a great deal of information that would arouse further curiosity. It happens, of necessity, but not terribly often.
More likely, if the President became aware of, and demanded, a specific detail (for reasons someone further down found insufficient) he might be stalled, it might become ‘temporarily misplaced or unavailable’ [hey, it happens - for what we are told in hindsight were benign reasons], or he might be given a watered down or misleading answer - e.g. if an impetuous President wanted to know the details about the source (the Polish colonel) behind key info “as a bargaining chip” for an upcoming summit (Presidents have, indeed, unwisely revealed details in summits) he might be given info about less sensitive sources that corroborated much or most of it. How would he know? The responsible official(s) might even tell themselves that that had turned over “a” source of that information, if not “the” (first or most reliable) source.
There have been reported accounts that suggest this happened in the Carter Administration. [He was particularly disliked in the CIA, and his DCI Stansfield Turner was respected but not considered an ‘insider’ DCI to the extent that, say, Reagan’s DCI William Casey, a former OSS officer, was]
Due to the 20 year (or more) limit, I don’t think you’ll find many people here willing to talk about incidents in administrations more recent than Carter.
There are at least two separate questions here. The first is legal, the second is practical. On a practical level, as KP notes,
I think that it is extremely likely that the CIA, the NSA, and the Military, can and do in practice keep information from the President.
The legal question, though, is different. The power to classify information, and to restrict access to it does not trump the Constitution, which is the Surpeme Law of the land. Under the Constitution, the executive power of the United States is vested in the President. Furthermore, the President is the Commander in Chief of the Armed Forces. In practice, someone might keep information from the President, but no one would have the legal authority to tell him that he (or she) did not have sufficient security clearance to see the information. Everything I’ve read about the CIA is consistent with the picture painted by KP, to wit, that many of the leaders of the CIA view the President with suspicion. But to my mind this speaks to their disrespect for the Constitution (something they have frequently been accused of), rather than a reasonable interpretation of the law.
In the film Independence Day they raised the concept (discussing presidential knowledge of Area 51, I think) of “plausible deniability” 
I guess there might be some mileage in the idea that having your the president genuinely able to say “I knew nothing about that” might have its benefits, particulary with regard to certain unpaletable programmes carried out by an administration?