It's normally applied to a version of events that a group of people believe to be true in direct conflict to the official version. Two well known examples of conspiracy theories are that man did NOT land on the moon but all the televised lunar landings were in fact an elaborate hoax, and that Roswell was not a Project MOGUL weather balloon carrying prototype spy gear but an alien landing on the Earth.
It should be noted that conspiracy theorists often have to ignore available facts in order to promote their beliefs. For example, the technology to fake the Apollo flights, moon rocks, and video, etc. does not yet exist, let alone exist in 1969. And all the hard evidence at Roswell (photos) are of Project MOGUL wreckage.
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A conspiracy is where a group of people plan a secret task that is only known to selected people.
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A conspiracy theory:
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The main characters in the movie "Conspiracy Theory" are Mel Gibson, Julia Roberts, and Patrick Stewart.
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The Apollo Moon landing hoax. While I agree with the above poster that the Moon Landing is quite a common theory, I would argue the Kennedy assassination is the most well known conspiracy theory.
Judeo-Bolshevism is an antisemitic conspiracy theory that claims that Communism is a Jewish conspiracy. The Wikipedia article on the subject (as accessed on 8 May 2009) is quite good. Please see link.
Possibly however it is a conspiracy theory, he was apparently funded by the CIA.