As there are people who don't have access to Twitter, here is a summary with links:
Jesse Walker: "People debate whether it's fully proven, but this may be the clearest-cut case of a story that was described as a conspiracy theory when I first encountered it and now has mainstream historians endorsing it: https://www.nytimes.com/2017/01/02/us/politics/nixon-tried-to-spoil-johnsons-vietnam-peace-talks-in-68-notes-show.html
@ValoisDuBins: "Operation Gladio is about the only one I can think of. It arguably stands as the exception that proves the rule." https://en.wikipedia.org/wiki/Operation_Gladio (Includes stuff RAW wrote about).
Miguel Madeira: "The death of the Portuguese Prime Minister Sá Carneiro have being an assassination? It is not 100% established, but today is ab hypotheses much more accepted in the mainstream than in the last century, where it was considered a conspiracy theory." https://en.wikipedia.org/wiki/Francisco_de_S%C3%A1_Carneiro
Several mentioned the Gulf of Tonkin incident, which included a second "attack" that was not real: https://en.wikipedia.org/wiki/Gulf_of_Tonkin_incident