I actually, believe it or not, got a few hostile responses from dudes who actually insisted that there has *never* been an instance, anywhere, any time, any place, of something that has been considered a "way out there, wacko conspiracy theory" that has been later proven to be actually correct and true.
I was taken somewhat aback by this, as there are ample evidences of this, apparently no one has taken the time to assemble it all into one place with all of the appropriate cites, etc.
Well, that is what I'm going to attempt to do here. I plan on having an email address that you can send info to if you'd like, and I myself will do some research and will post my findings here.
For the time being, here is a post from Usenet discussion newsgroups that was in answer to the question "Has there ever been any conspiracy theories that later turned out to be the true version of events?" It lists some of the things that were at one time dismissed as "conspiracy theory" but were later proven to be true, upon release of later information/documentation.
One thing that is not mentioned in this post is the myth that has grown up over the years around "McCarthyism". Recently released KGB documents and other Russian documents show that McCarthy was basically correct in most of his charges in the 1950s, and that the Rosenbergs really were spies and compromised our security in the 1950s.
Anyway, many people have vested interests in keeping the truth away from the public. Many times today's "conspiracy theories" end up being tomorrows facts.
Here's the Google post responding to the question "Have there been any conspiracy theories that were later proven to be true, and a true version of the facts?"
This is a bit of a problem, because once it is out and clear, it isnot a conspiracy theory anymore. Most of the theories I've collectedare quite familiar, nothing up Pink's alley of 15th century'sconspiracies.
Some of the most prominent political scandals in US history began as aconspiracy theory and turned out to be true; Wikipedia(http://www.wikipedia.com/) lists some of these:
"The United States Department of Defense Information Awareness Office(IAO) has many similarities to conspiracy theories. First, its avowedpurpose is to gather and correlate information on ordinary citizensfor the purpose of predicting terrorism and other crime. Second, itslogo depicted the eye in the pyramid, a symbol associated withIlluminati and Masonic representations of power or divinity, casting abeam over the globe of the Earth. This has since been changed. Theoriginal logo is still widely available on the internet, however.Lastly, the name "Iao" is a Gnostic word for God, used in the GoldenDawn and Thelema among others. 
The Mafia was essentially completely unknown to outsiders until JoeValachi revealed them in 1963.
Declassified papers as well as legal inquiries have shown that the CIAwas involved in many coup d'??tat, including the overthrow of JacoboArbenz Guzman and Salvador Allende as well as into terrorist action,for instance in Italy
From the 1950s to the 1970s, the CIA and the U.S. Army operated aresearch program into mind control, codenamed MKULTRA. In thisprogram, CIA agents gave LSD and other drugs to unwitting andunconsenting victims, in an effort to devise a working "truth serum"and/or mind-control drug. MKULTRA was uncovered by Presidential andCongressional research committees in 1975, and discontinued at thattime. Many prominent writers and drug figures were first exposed toLSD under this program, including Ken Kesey of the Merry Pranksters,Timothy Leary, Allen Ginsberg, Baba Ram Dass (Richard Alpert) andfuture 'Unabomber' Theodore Kaczynski. A source on this is the book"Acid Dreams" by Bruce Shalin and Martin A. Lee.
ECHELON is a communications interception network operated by theUnited States, the United Kingdom, Canada, Australia and New Zealand.It is designed to capture telephone calls, fax and e-mail messages.New Zealand has openly admitted the existence of Echelon, and theEuropean Union commissioned a report on the system.
In the 2003 Iraq War, Iraqi resistance was strong at first and thencollapsed suddenly. A conspiracy theory emerged in Iraq and elsewherethat there had been a safqah" ?? Arabic for: a secret deal ? ? betweenthe US and the Iraqi military elite, wherein the elite were bribed tostand down. This conspiracy theory was ignored or ridiculed in the USmedia.In late May, 2003, General Tommy Franks, who had been the head of theUS forces in the conflict, confirmed in an interview with Defense Newsthat the US government had paid off high-level Iraqi militaryofficials and that they had stated that "I am working for you now".How important this was to the course of the conflict was not entirelyclear at the time of this writing (May 24, 2003).
Operation Northwoods, a CIA plot to commit acts of apparent terrorismand blame them on Cuba to encourage support for a war, was longconsidered to be nothing but a conspiracy theory ? until the project'sdocuments were declassified and published.
The Tuskegee Study of Untreated Syphilis in the Negro Male. For aperiod of 50 years, the US Government used some members of the blackpopulation of a town in Alabama to observe the effects of untreatedsyphilis. The participants were not asked to participate and were nottold they were being untreated for their syphilis.
The US Federal Reserve lends money to the government at interest. Whenthis happens, money floods the market, and creates the "hidden tax" ofinflation. This scheme has had similar effects with the previousnational banks, and been predicted by conspiracy theories prior to itsimplementation in 1913. Also, although the word "federal" is used, theUS Government does not own the Federal Reserve and has limited controlof its operations.
The Bilderberg Group, an annual convention of Western political andeconomic elites, actually does exist. It is thought of as a modern-dayIlluminati-style conspiracy by some, where persons with power discussand arrange control of the world."
Martyn Jones also considers other as a true conspiracies, mostdistinctively Watergate (Washington Post on Watergate:<http://www.washingtonpost.com/wp-srv/national/longterm/watergate/front.htm>; "Watergate.net" <http://www.watergate.info/>), but also
"British Premiere Margaret Thatcher ordered the Royal Navy warshipthat had patrolled the coast of The Falklands since the 60s tostand-down immediately prior to the islands invasion by an Argentineanexpeditionary force".
"Although many juvenile republicans and arm-chair supporters stillscoff at the idea that the Clintons were the target of a vastconspiracy, overwhelming material evidence and the testimonials ofmany participants on all aides indicates otherwise." (SOURCE: MartynJones, <http://www.newsgarden.org/columns/martycolumns2.shtml> ;However, I would say that "Monicagate" in itself *is* a conspiracyturned out to be true: who would think the president would do such athing?)
One of the most fun people to have conspiracies about, that in turnwould turn out to be absolutly true is Imelda Marcos. You have toworship that woman:
- Yes, she did try to have a porn film festival in Manila and calledthe Cardinal "gay" because he opposed it;
- Yes, she did send the Filippino secret security forces to beat upthe Beatles at the Manila Airport, because the fab-four did not wantto meet her after their show in the Philippines;
- Yes, she did have so many shoes;
I get all of that (and many other unbelievable stories about theMarcoses: he made up his record in the underground against theJapanese occupation, for example) from a book, not from the Internet:James Hamilton-Paterson, "America's Boy" (Granta).
Still in Asia, this article claims to have another, made-in-Seoulreal-life conspiracy:Aidan Foster-Carter, "North Korea's missiles: just so convenient",Asia Times January 09, 2001<http://www.atimes.com/koreas/CA09Dg01.html>
I can't verify the validity of the claims made in Asia Times, becauseI am not that acquinted with the story.
Another claims of "no smoke without fire" is made by another reputablebody, the Canadian CBC:Fifth Estate, Conspiracy Theories (regarding 9/11)<http://www.cbc.ca/fifth/conspiracytheories/> This site deals mostly with the claims on Bush-Saudi connections, andclaims that although the theories continue to be just that - theoriesand not facts - there are some supporting evidences.
However, I could add one more things that was also found to be true(thought I am not sure how much of a conspiracy it has been):
The FBI established and operated COINTELPRO, designed to monitor andsabotage the operations of social movements deemed "subversive"(See Prof. David Cunningham's book "There's Something Happening Here"U. California Press about it; and see his homepage:<http://www.brandeis.edu/departments/sociology/cunningham.html>);
I hope this answered your question. There are probably some otherevents that people consider as a "conspiracy theory" and were found tobe true; others would claim that by definition, a conspiracy theorycannot be found to be true (but cannot be debunked either), becausethen the whole conspirative tone would disappear. My search strategywas to search for the term "conspiracy theory" with other terms likelyto appear in the text such as "to be true". I also searchedSnopes.com, but all of the conspiracy theories mentioned there arelabled as "false".