My main gripe with the term 'conspiracy theory' is in how it is used.
Official history may be examined from every possible avenue and angle. Libraries full of history books on the same subject are testimony to that. Conspiracy theories are meant to be instantly put aside, never to be considered again.
No, that is not how historians work. If history is written by the winners (who aren't always those who thought that they won at the time), then there is practically a duty to investigate what stories were left untold.
The term 'conspiracy theory' tends to be injected into the debate in the same way as other stop words, like 'un-American', 'paedophilia' or 'Nazi'. They are words or phrases which you can't argue beyond without appearing somehow ridiculous, naive, criminally insane or traitorous. It's a personal attack to divert attention away from what you're actually saying.
At the very least, that's bad debating skills. At worse, it's forcing conformity into a single point of view.
Moreover, by using the word 'theory', it implies that no evidence has been produced at all; or that nothing is proven by that which is on the table. How many people, with just a casual or passing interest in the story, actively evaluate the facts for themselves? There's an assumption that the person dismissing the case has already done that and found the evidence lacking.
Am I saying that every version of events labelled a 'conspiracy theory' is actually true? No, I'm not. But I am arguing that we'll never know, unless we afford them all the same scrutiny as we do the commonly accepted versions.
Under the strong spotlight of the evidence, many will wither away as unsupported paranoia. But others may not. As Mulder, in The X-Files, put it so succinctly, the truth is out there.