As a child I always thought it meant you were going to get a boyfriend. I knew it as
One for sorrow
Two for joy
Three for a letter
Four for a boy
Five for silver
Six for gold
Seven for a secret never to be told.
It's my view that it was always 3 for a letter until the children's TV programme Magpie used it as a theme song. As they issued badges to viewers they changed it to girl and boy so both sexes could benefit.