"So Mote it Be" is one of those archaic phrases that many people in the Pagan community use, yet its origins may not be Pagan at all.
According to Webster's dictionary, the word mote was originally a Saxon verb which meant "must." It appears back in the poetry of Geoffrey Chaucer, who used the line The wordes mote be cousin to the deed in his prologue to the Canterbury Tales.
Occultist Aleister Crowley used "So mote it be" in some of his writings, and claimed it to be an ancient and magical phrase, but it's possible he borrowed it from the Masons. In Freemasonry, "So mote it be" is the equivalent of "Amen" or "As God wills it to be." Gerald Gardner, the founder of modern Wicca, was also known to have Masonic connections, although there's some question about whether or not he was a Master Mason as he claimed to be. Regardless, it's no surprise that the phrase turns up in contemporary Pagan practice, considering the influence that the Masons had on both Gardner and Crowley.
In modern Wiccan traditions, the phrase often appears as a way of wrapping up a ritual or magical working. It's basically a way of saying, "And so it shall be."