He came to us with some gender identity confusion, for several reasons. (1) There were NO adult males at the orphanage, EVER (even all the doctors, truck drivers, etc that he encountered were all women) (2) He was delicate for medical reasons (endless series of ear and upper respiratory infections) and had a club foot, so he couldn't do all that bumble-puppy rough-and-tumble play, never "ran with the pack" with other boys; (3) meanwhile, he was cute and funny (darling little Asian amongst all the other orphans, who were Slavic Russians) and the girls always liked it when he played with them---
So when he came to us --- he was almost five --- he always wanted to dress up like a girl, he wanted to be the girl character in the video game (Princess Peach instead of Super Mario or whatever), he displayed distractingly feminine mannerisms, like a sashaying, hip-swaying walk, a kind of toss of his head and flirtatious fluttering of his eyelashes; even sometimes a high, simpering tone of voice that really bothered me.
My husband and I consulted some of the books cited by other FReepers above, about affirming and strengthening a boy's gender identity. We made sure he got (and gets) plenty of daddy-time with Mr. Don-o. We encouraged him to (literally) run in packs with his fellow home-schooling guy friends --- fortunately we're in the kind of neighborhood that boys can safely "run around" in.
As for the feminine dressing and the mannerisms, my husband and I thought it wisest just to let that pass without any comment one way or the other (except that I forbade him to get into my closet and flounce around in my blouses and skirts, etc.!) Instead, we accentuated the positive: encouraged him to wear Dad's hats, told him how great he looked in his older brother's T-shirts (even when they came down to his knees) etc.
Now he's 13 and he seems to be doing fine. A kind, comical, affectionate and sensitive personality; no more flouncing, simpering and sashaying; more interested in Marc Antony's sword and armor than in Cleopatra's flowing frocks; just a happy, XY-and-proud-of-it, testosterone-nuanced boy-o-boy. Good heavens, we're thankful for that.
An old thread for certain!~ I was led to this by a couple other threads, read your fascinating post and wondered how you were making out with your son four years later?