What would really be useful would be example of conspiracy theories that were accepted by a fringe group, rejected by the mainstream (for at least a decade, say), and ultimately found to be true. Maybe the COINTELPRO would qualify for this - were some of the targeted groups complaining about FBI targeting them?

Interesting edge case is the whole McCarthy stuff - he was right that there was a quite a bit of communist spying, but he appeared to have no evidence whatsoever for this (and his specific accusations were mostly random). Does accidentally being correct count? Or is this more another case of "reverse stupidity isn't intelligence"?