Nearly all monotheistic religions refer to God as a "He", as a male father-figure. This is because the creators of those religions were themselves all male1. Modern new religions and movements such as Wicca and the New Age do not fall into the same patriarchal trap. The gender of god, or the determination of which gendered pronoun we should use, is one of the major illogical assumptions about God that people frequently make. God has no gender. It does not reproduce. It makes no sense biologically, sexually or culturally to call the creator of all genders and species by the particular gender of a particular species. He and She are appropriate pronouns for species with two sexes, not for the God of the Universe. We have no right to assume to call God by any gender based on the characteristics of human roles. God is not a "He" or a "She", but an It.
Biology: An all-powerful, singular creator God that is the first cause, would have no gender. It did not evolve into a God, it did not have parents and it does not have or need sexual organs. If it reproduced, it would be by the magic of miracle, not by sexual intercourse. God does not have genitals or anything similar to X and Y chromosomes: All these things are the product of the long progression of evolution, products of creation. The creator itself cannot be gendered.
Gender Roles: To call God a "he" is a projection of human emotions and characteristics. To call it "he" or "she" is to limit God to our perceptions of gender roles as they pertain to the human species. This is simply inappropriate and weird. Some theists believe that God sometimes uses magic in order to have children. This would make it female. Others believe that it is male. Whatever the specific terminology of any tradition, it stands that it is only logical to call god "it" and not "he" or "she". Whether If God is everywhere and knows everything and can take any form, or is perhaps the entire universe itself, God must be omni-sexual. There is no pronoun for omnisexuality. Neither a "he" nor a "she" pronoun makes sense.
Comparative Religion: Many consider God to be a male father figure, many consider it to be a female mother figure. To avoid giving either group the privilege of using their particular terminology for God, use the gender-neutral term of it.
Epistemology and Humility: I do not know God's gender. It is not offensive to an all-knowing God to admit that you don't know what gender it is. It would be offensive to assume to call an all-powerful being by a Human gender. Nature has endowed species with various styles of sexualities and genders, and it seems that a Creator-God would be above it all. Therefore, it is most humble, least assuming and reflects its nature best if we avoid using gendered pronouns to refer to a monotheistic God.
The Human Element: Gender Politics and the Technicalities of English. It is potentially offensive (and certainly presumptive) to womankind to call a theorized creator male, and it is offensive to mankind to call it female. It is not offensive to use gender-neutral language. It is certainly not offensive to God, who itself has no gender and, I would concede, probably has far more pressing concerns than the taxonomic systems of English linguists.
It is not popular amongst traditional religionists to use gender-neutral language, because most religion has been patriarchal. But many New Religious Movements and some other obscure corners of Human spirituality buck this trend. In the New Age religion of Eckankar their sacred name for God is Sugmad, which they stress "is neither masculine nor feminine"2. The Hermetic Order of the Golden Dawn (an occult magical group founded towards the end of the 19th century) recognized the divine as having feminine aspects as well as male3. Kabbalists (mystics and occultists who indulge in the Kabbalah/Qabbala) teach that "En Sof was neither male nor female. It was an 'It' that became a 'Thou' to the mystic at the end of the process of emanation"4.Divinity in Wicca is seen as both male and female (typically as the Horned God and Mother Goddess5), as are the general forces of nature which emanate from the male and female principal6,7, and these two sides complement one another8,9.