Witch Trials are infamous events in history in which witches are hunted down by both Witch Hunters and townspeople, and executed. The witches are either hung, immersed in water or burned at the stake. There were two major Witch Trials in American history; the Salem Witch Trials between 1690-1692, and the 2009 Witch Trials, which were started by Phoebe.
The Salem Witch Trials
The Salem witch trials were a series of hearings before local magistrates followed by county court of trials to prosecute people accused of witchcraft in Essex, Suffolk, and Middlesex counties of colonial Massachusetts, between February 1692 and May 1693. During the trials, many people (both male and female), even children, were hanged or drowned, while one man died from crushing. Often it would be innocent people, convicted of practicing magic, whilst they never even had anything to do with the so-called Dark Arts.
To prove that they were truly innocent, the convicted would be 'floated' by being tied up and thrown in a river. If they sank, they would be declared human, if they floated, they were declared a witch.
Melinda Warren, the Charmed Ones' great, great, great, great, great Grandmother, was burned at the stake during the Salem Witch Trials, when her lover and, unknown to her at the time, warlock Matthew Tate revealed her to be a witch after stealing her powers. It was on the stake, that Melinda prophesied the legacy of the Charmed Ones.
The 2009 Witch Trials
In 2009, a baseball player named Cal Greene murdered a dear friend of Phoebe - which we find out was her boss at The Bay Mirror, Elise Rothman. A technicality set him free and in revenge, a furious and outraged Phoebe killed Cal. According to Leo, that's when she crossed the line from protecting the innocent to punishing the guilty. However, unknown to her, this was presumably caught on tape and Phoebe was exposed as a witch by a man called Nathaniel Pratt, the local DA. This is what started the 2009 Witch Trials with Pratt at the helm. Prue and Piper were both save. Pratt had checked them out but didn't suspect anything. Still, they were both in danger as they had to be very careful with their powers, as well as Piper's daughter, Melinda.
Although Phoebe and her sisters traveled to 2009 to try and rescue her, Phoebe didn't allow them to and said that she had to die, for she had killed a man, an innocent. She explained that "the wrong thing done for the right reason is still the wrong thing" and thus let herself be burned on the stake. This was the lesson the sisters had to learn and before Phoebe was completely burned, the Elders had sent them back to 1999. Because of the Witch Trials started by Phoebe, many convicted witches and innocently accused people had been forced to go underground.
Modern Day Witch Trials
The Darklighter Rennek stole Leo Wyatt's knowledge which he acquired during his various magical transformations (Whitelighter, Elder, and Avatar) and used it to cause magic to switch sides: granting mortals supernatural powers and rendering magical beings that where on Earth at the moment of the switch, completely powerless.
Of what have been revealed, the government was already aware of magic and now blames the magical community for mortals having magic. The government created Magic Squads to track the source of magic and capture those who don't exhibit signs of magic, supposedly to experiment on them. 
- The season premiere of season 2 is called "Witch Trial" but it has in fact nothing to do with witch trials at all.
- The season 2 episode Morality Bites deals with the future witch trials started by Phoebe. They are referred to as the "2009 Witch Trials".
- The Salem Witch Trials ended in May 1693. The Book of Shadows was supposedly created by Melinda Warren during the same year.
- After Phoebe Halliwell had invoked the Power of Three, her older sister Piper watched a documentary on Mary Eastey; a woman in the 17th century who was convicted of practicing witchcraft. Before the townspeople could hang or burn her, she was struck by lightning upon entering a church.