Pretty good piece here
http://www.newworldorderreport.com/Articles/tabid/266/ID/980/33-Conspiracy-Theories-That-Turned-Out-To-Be-True-What-Every-Person-Should-Know.aspxThe first 15 (original link has links and videos):
1. The Dreyfus Affair: In the late 1800s in France, Jewish artillery officer Alfred Dreyfus was wrongfully convicted of treason based on false government documents, and sentenced to life in prison. The French government did attempt to cover this up, but Dreyfus was eventually pardoned after the affair was made public (an act that is credited to writer Émile Zola).
2. The Mafia: This secret crime society was virtually unknown until the 1960s, when member Joe Valachi first revealed the society's secrets to law enforcement officials. What was known was that organized crime existed, but not that the extent of their control included working with the CIA, politicians and the biggest businesses in the world.
3. MK-ULTRA: In the 1950s to the 1970s, the CIA ran a mind-control project aimed at finding a "truth serum" to use on communist spies. Test subjects were given LSD and other drugs, often without consent, and some were tortured. At least one man, civilian biochemist Frank Olson, who was working for the government, died as a result of the experiments. The project was finally exposed after investigations by the Rockefeller Commission.
4. Operation Mockingbird: Also in the 1950s to '70s, the CIA paid a number of well-known domestic and foreign journalists (from big-name media outlets like Time, The Washington Post, The New York Times, CBS and others) to publish CIA propaganda. The CIA also reportedly funded at least one movie, the animated "Animal Farm," by George Orwell. The Church Committee finally exposed the activities in 1975.
5. Manhattan Project: The Manhattan Project was the codename for a project conducted during World War II to develop the first atomic bomb. The project was led by the United States, and included participation from the United Kingdom and Canada. Formally designated as the Manhattan Engineer District (MED), it refers specifically to the period of the project from 1942–1946 under the control of the U.S. Army Corps of Engineers, under the administration of General Leslie R. Groves. The scientific research was directed by American physicist J. Robert Oppenheimer. The project's roots lay in scientists' fears since the 1930s that Nazi Germany was also investigating nuclear weapons of its own. Born out of a small research program in 1939, the Manhattan Project eventually employed more than 130,000 people and cost nearly US$2 billion ($22 billion in current value). It resulted in the creation of multiple production and research sites that operated in secret. With the total involved, this makes it one of the largest conspiracies in history. Entire towns were built for short periods of time, employing people, all under secrecy and top national secrecy at that. The government never admitted to it, the media never reported on it, and people had no idea for over 25 years. Project research took place at over thirty sites across the United States, Canada, and the United Kingdom. The three primary research and production sites of the project were the plutonium-production facility at what is now the Hanford Site, the uranium-enrichment facilities at Oak Ridge, Tennessee, and the weapons research and design laboratory now known as Los Alamos National Laboratory. The MED maintained control over U.S. weapons production until the formation of the Atomic Energy Commission in January 1947.
6. Asbestos: Between 1930 and 1960, manufacturers did all they could to prevent the link between asbestos and respiratory diseases, including cancer, becoming known, so they could avoid prosecution. American workers had in fact sued the Johns Manville company as far back as 1932, but it was not until 1962 that epidemiologists finally established beyond any doubt what company bosses had known for a long time – asbestos causes cancer.
7. Watergate: Republican officials spied on the Democratic National Headquarters from the Watergate Hotel in 1972. While conspiracy theories suggested underhanded dealings were taking place, it wasn't until 1974 that White House tape recordings linked President Nixon to the break-in and forced him to resign.
8. The Tuskegee Syphilis Study: The United States Public Health Service carried out this clinical study on 400 poor, African-American men with syphilis from 1932 to 1972. During the study the men were given false and sometimes dangerous treatments, and adequate treatment was intentionally withheld so the agency could learn more about the disease. While the study was initially supposed to last just six months, it continued for 40 years. Close to 200 of the men died from syphilis or related complications by the end of the study.
9. Operation Northwoods: In the early 1960s, American military leaders drafted plans to create public support for a war against Cuba, to oust Fidel Castro from power. The plans included committing acts of terrorism in U.S. cities, killing innocent people and U.S. soldiers, blowing up a U.S. ship, assassinating Cuban émigrés, sinking boats of Cuban refugees, and hijacking planes. The plans were all approved by the Joint Chiefs of Staff, but were reportedly rejected by the civilian leadership, then kept secret for nearly 40 years.
10. 1990 Testimony of Nayirah: A 15-year-old girl named “Nayirah” testified before the U.S. Congress that she had seen Iraqi soldiers pulling Kuwaiti babies from incubators, causing them to die. The testimony helped gain major public support for the 1991 Gulf War, but — despite protests that the dispute of this story was itself a conspiracy theory — it was later discovered that the testimony was false. The public relations firm Hill & Knowlton, which was in the employ of Citizens for a Free Kuwait, had arranged the testimony. It turned out that she had taken acting lessons on request of the CIA and was actually the niece of a major politician in Kuwait. Nayirah was later disclosed to be Nayirah al-Sabah, daughter of Saud bin Nasir Al-Sabah, Kuwaiti ambassador to the USA. The Congressional Human Rights Caucus, of which Congressman Tom Lantos was co-chairman, had been responsible for hosting Nurse Nayirah, and thereby popularizing her allegations. When the girl's account was later challenged by independent human rights monitors, Lantos replied, "The notion that any of the witnesses brought to the caucus through the Kuwaiti Embassy would not be credible did not cross my mind... I have no basis for assuming that her story is not true, but the point goes beyond that. If one hypothesizes that the woman's story is fictitious from A to Z, that in no way diminishes the avalanche of human rights violations." Nevertheless, the senior Republican on the Human Rights Caucus, John Edward Porter, responded to the revelations "by saying that if he had known the girl was the ambassador's daughter, he would not have allowed her to testify."
11. Counter Intelligence Programs Against Activists in the 60s: COINTELPRO (an acronym for Counter Intelligence Program) was a series of covert, and often illegal, projects conducted by the United States Federal Bureau of Investigation (FBI) aimed at investigating and disrupting dissident political organizations within the United States. The FBI used covert operations from its inception, however formal COINTELPRO operations took place between 1956 and 1971. The FBI's stated motivation at the time was "protecting national security, preventing violence, and maintaining the existing social and political order." According to FBI records, 85% of COINTELPRO resources were expended on infiltrating, disrupting, marginalizing, and/or subverting groups suspected of being subversive, such as communist and socialist organizations; the women's rights movement; militant black nationalist groups, and the non-violent civil rights movement, including individuals such as Martin Luther King, Jr. and others associated with the Southern Christian Leadership Conference, the National Association for the Advancement of Colored People, the Congress of Racial Equality, the American Indian Movement, and other civil rights groups; a broad range of organizations labeled "New Left", including Students for a Democratic Society, the National Lawyers Guild, the Weathermen, almost all groups protesting the Vietnam War, and even individual student demonstrators with no group affiliation; and nationalist groups such as those "seeking independence for Puerto Rico." The other 15% of COINTELPRO resources were expended to marginalize and subvert "white hate groups," including the Ku Klux Klan and National States' Rights Party. The directives governing COINTELPRO were issued by FBI Director J. Edgar Hoover, who ordered FBI agents to "expose, disrupt, misdirect, discredit, or otherwise neutralize" the activities of these movements and their leaders.
12. The Iran-Contra Affair: In 1985 and '86, the White House authorized government officials to secretly trade weapons with the Israeli government in exchange for the release of U.S. hostages in Iran. The plot was uncovered by Congress in 1987.
13. The BCCI Scandal: The Bank of Credit and Commerce International (BCCI) was a major international bank founded in 1972 by Agha Hasan Abedi, a Pakistani financier. The Bank was registered in Luxembourg. Within a decade BCCI touched its peak, it operated in 78 countries, had over 400 branches, and had assets in excess of US$ 20 billion making it the 7th largest private bank in the world by assets. In the late 1980's BCCI became the target of a two year undercover operation conducted by the US Customs Service. This operation concluded with a fake wedding that was attended by BCCI officers and drug dealers from around the world who had established a personal friendship and working relationship with undercover Special Agent Robert Mazur. After a six month trial in Tampa, key bank officers were convicted and received lengthy prison sentences. Bank officers began cooperating with law enforcement authorities and that cooperation caused BCCI’s many crimes to be revealed. BCCI came under the scrutiny of regulatory bodies and intelligence agencies in the 1980s due to its perceived avoidance of falling under one regulatory banking authority, a fact that was later, after extensive investigations, proven to be false. BCCI became the focus of a massive regulatory battle in 1991 and was described as a "$20-billion-plus heist". Investigators in the U.S. and the UK revealed that BCCI had been "set up deliberately to avoid centralized regulatory review, and operated extensively in bank secrecy jurisdictions. Its affairs were extraordinarily complex. Its officers were sophisticated international bankers whose apparent objective was to keep their affairs secret, to commit fraud on a massive scale, and to avoid detection."
14. CIA Drug Running in LA: Pulitzer Prize Award winning journalist Gary Webb exposed this alongside LAPD Narcotics Officer turned whislteblower and author Michael Ruppert, CIA Contract Pilot Terry Reed, and many others. In August 1996 the San Jose Mercury News published Webb's "Dark Alliance", a 20,000 word, three-part investigative series which alleged that Nicaraguan drug traffickers had sold and distributed crack cocaine in Los Angeles during the 1980s, and that drug profits were used to fund the CIA-supported Nicaraguan Contras. Webb never asserted that the CIA directly aided drug dealers to raise money for the Contras, but he did document that the CIA was aware of the cocaine transactions and the large shipments of cocaine into the U.S. by the Contra personnel. "Dark Alliance" received national attention. At the height of the interest, the web version of it on San Jose Mercury News website received 1.3 million hits a day. According to the Columbia Journalism Review, the series became "the most talked-about piece of journalism in 1996 and arguably the most famous—some would say infamous—set of articles of the decade."
15. Gulf of Tonkin Never Happened: The Gulf of Tonkin Incident is the name given to two separate incidents involving the Democratic Republic of Vietnam and the United States in the waters of the Gulf of Tonkin. On August 2, 1964 two American destroyers engaged three North Vietnamese torpedo boats, resulting in the sinking of one of the torpedo boats. This was also the single most important reason for the escalation of the Vietnam War. After Kennedy was assassinated, the Gulf of Tonkin gave the country the sweeping support for aggressive military action against the North Vietnamese. The outcome of the incident was the passage by Congress of the Gulf of Tonkin Resolution, which granted President Lyndon B. Johnson the authority to assist any Southeast Asian country whose government was considered to be jeopardized by "communist aggression". In 2005, an internal National Security Agency historical study was declassified; it concluded that USS Maddox had engaged the North Vietnamese on August 2, but that there may not have been any North Vietnamese vessels present during the engagement of August 4. The report stated “It is not simply that there is a different story as to what happened; it is that no attack happened that night…” In truth, Hanoi's navy was engaged in nothing that night but the salvage of two of the boats damaged on August 2. In 1965, President Johnson commented privately: "For all I know, our Navy was shooting at whales out there." In 1981, Captain Herrick and journalist Robert Scheer re-examined Herrick's ship's log and determined that the first torpedo report from August 4, which Herrick had maintained had occurred—the "apparent ambush"—was in fact unfounded. In 1995, retired Vietnamese Defense Minister Vo Nguyen Giap, meeting with former Secretary of Defense McNamara, categorically denied that Vietnamese gunboats had attacked American destroyers on August 4, while admitting to the attack on August 2. In the Fall of 1999, retired senior CIA engineering executive S. Eugene Poteat wrote that he was asked in early August 1964 to determine if the radar operator's report showed a real torpedo boat attack or an imagined one. In October, 2005 the New York Times reported that Robert J. Hanyok, a historian for the U.S. National Security Agency, had concluded that the NSA deliberately distorted the intelligence reports that it had passed on to policy-makers regarding the August 4, 1964 incident. He concluded that the motive was not political but was probably to cover up honest intelligence errors.