There are two items of 'common knowledge' that really bug me as a history graduate. The first (which I won't discuss here) is the idea that 'everyone' believed the world was flat during the time of Christopher Columbus. How people continue to believe that when navigational instruments of the time required a knowledge of a circular earth in order to work astounds me (and yes, I'm sure some peasantry in Europe didn't know the earth was round and probably wouldn't have cared either. My complaint is that the people who were in charge WOULD have know and WOULD have cared).
The second historical 'knowledge' is the idea that the witch hunts were a medieval invention brought forth from the smelly dirty time where people had no sense of reality. Luckily we were saved from this nasty brutish existence by that wonderfully golden age the renaissance.
I just finished an incredible book, Europe's Inner Demons by Norman Cohn. In it, he examines where the ideas of the witch hunts come from. Yes, the roots of the beliefs came out of the middle ages (based off of beliefs attributed to heretics, folkloric beliefs and the practice of ritualistic magic) and yes, there were a few isolated witch hunts (or, more accurately, heresy hunts in which heretics - proved or not - were burned singly and en mass). But the witch hunts from popular imagination did not take place during the middle ages. They were a later invention. Read the book to find out his reasoning. It's extremely well documented and carefully considered. He examines the secondary sources from which the idea that the middle ages started the witch hunts and then examines the primary sources they quote in order to check their validity. What he discovers is quite remarkable, and debunks much that is considered 'common knowledge' with regards to the witch hunts.
About how the witch hunts actually started I'll quote a little from his book, page 215. Information in [ ] brackets is supplied by me to explain things the author explained earlier.
"Almost throughout the Middle Ages - very generally until the thirteenth century, in some parts of Europe even to the fifteenth century - the accusatory form of criminal procedure obtained. That is to say, the legal battle was fought out not between society and the accused [as was the case in the witch hunts and heretic trials, where the Church was often the accuser and could employ torture to achieve 'confessions'. This was also the case when asking an accused to denounce others, something that wouldn't happen in trials brought forth by an individual.], but between the accused and a private person who accused him. In this respect there was no difference between a civil and a criminal case; in the latter as in the former the individual complainant was responsible for finding and producing proofs such as would convince the judge.
The accusatory procedure was derived from Roman law, and it retained all those features which had characterized it under the later Empire. By and large it favoured the accused rather than the accuser. The accuser was obliged to conduct the case himself, without the assistance of prosecuting counsel. Moreover, if he failed the convince the judge he was likely to suffer as heavy a penalty as would have been visited upon the accused if he had been convicted. This was known as the talion.
The intention behind the talion was simply to discourage malicious or frivolous accusations, but the effect was far more sweeping. How was the law to distinguish between a mere mistake and deliberate calumny? In practice it seldom distinguished; everyone knew that an unsuccessful complainant would almost certainly be penalized, whatever his motives. ...
Everything possible was done to impress the would-be accuser with the risks involved. When notifying the judge of the proposed action, the accuser had to give a written undertaking to provide proof and, if the proof were found inadequate, to submit to the penalty of the talion as a culminator. And that was not all: once the inscription had been accepted by the judge, the accuser could not withdraw without incurring the penalty of the talion."
Now, this does not mean people were never tried for maleficium (witchcraft) and punished. Nor does it mean the middle ages were an entirely lawful time, as lynching of suspected witches sometimes and maybe even often took place. There are a few isolated group trials of heretics and others performed during the middle ages by religious fanatics. But by and large the majority of witch hunts as considered in popular belief were, at best, late medieval and renaissance inventions.
Mr. Cohn concludes his work with the idea that later Ecclesiastes and bureaucrats were more willing to accept the truth behind accusations of witchcraft and evil doing in ways that those of earlier times were not. Allowing for miscarriages of justice where individuals were forced into confessions and then forced to denounce family and friends as being participants in an underground movement wherein the practitioners had denied Christ and begun worshiping the
Devil and performing malicious acts upon their neighbours.
At any rate, the book is fabulous - though it is fairly dry and scholarly - and the topic is fascinating.
Wikipedia's entry on the witch hunts is accurate and is a great jumping off point for learning more.