Thanks, that's a nice askreddit thread. A lot of these have the same problem though, which is that I have trouble believing (and have no idea how to find evidence, since they were well pre-internet) that these were conspiracy theories before they were revealed.
(I note now that I didn't actually mention, in my comment, that by "was a conspiracy theory" I don't just mean "sounds crazy" but rather "sounded crazy and there were actually people saying it". I'm not interested in every insane thing secret agencies did*, I'm interested in stuff people successfully predicted.)
*well, I am, but it's not what the question is about
Oh, the lab leak/zoonosis debate is a good thought, but I don't think it counts as a conspiracy - if I search for news articles from before 2022 mentioning it, I immediately find, say, this BBC article from 2020 that treats lab leak seriously, so it was a mainstream-ish idea quite early on. This seems to match with my own memories, I've seen lab leak being discussed in 2022 and I think even earlier.
In general, though, there's probably some good COVID-related example, even if I can't think of one immediately (I think it's pretty disingenuous how media demonized every prospective COVID drug, especially ivermectin - but they did turn out to be ineffective against the virus itself, and I don't think there were any conspiracies about the drugs that ended up actually working, like Paxlovid).