GAOTU is a shorthand way of refering to God, The Great Architect of the Universe, used by Freemasons. Because Freemasonry is made up of men of many different faiths refering to God using a name, such as Christ, Brahma, or Jehovah, would be considered divisive. If we prayed in the name of Christ, non-Christians would feel left out. If we prayed in the name of Brahma, non-Hindus would feel left out. Therefore Freemasons use GAOTU as a way of refering to God.
Some might think it strange that using the name of Christ or Jehovah could be considered divisive. This has lead to many anti-masonic groups charging that Freemasonry is anti-christian because they do not pray in the name of Christ. When in fact Freemasonry just seeks to be inclusive.
When used in Masonic Ritual the full phrase is used, The Great Architect of the Universe. The short hand is never pronounced. GAOTU is not the exclusive means of refering to God in Freemasonry though. Masonic Ritual refers to God in many ways, but they are all characterized by their general character so as to be inclusive.