The modern witch hat in its current form, such as the Luella runway pic from her Fall '08 collection, was widely pictured beginning in Victorian times. Until then, it was basically a memory of the past. I believe the origins are very ancient, and have magical and religious significance. I'm not alone in this belief, but it's a controversial theory and one that will never be proven one way or another. So feel free to take from this what you will and come to your own conclusion. In a nutshell:
Along the Silk Road in China a woman's mummy was discovered and dated to the mid 1st millennium BCE. One of her adornments was a tall dark felt hat with two conical peaks. Yet another female body excavated also wore a very tall, conical hat. Chinese references to Western magicians date back to 1500 BCE.
Ancient Persian magicians wore a tall pointy hat. Egyptian pharaohs had a tall dome piece, as did Hittite kings and queens. Certain ancient Roman priestesses and priests assigned to a particular god or goddess wore a conical cap. A coin from the Etruscan city of Luna (ahem) bears the image of a woman (thought to be the goddess Diana, patron of witches) wearing a conical hat. Bishops, the pope, present day priests in Tibet- all have upward- reaching head gear.
A bit more current were fashion trends of Europe. Loads of wonderful headgear was worn in
the Middle Ages and Renaissance periods. In the sixteenth and seventeenth centuries popular style trickled out into the country and folk picked up on the tall hat look. But then of course the courtly fashion had changed, peasants (pagans) were despised and accused of deviltry, and they were pointed at wearing their pointy hat. This continues with the persecution of Quakers in America; recall the "pilgrim" hat?