I also had the same situation happen here at the beginning of the summer when we hired a temp file clerk. She wore a lot of perfume and even with our windows open it was stiffling. We had a meeting with her to discuss things regarding her position, hours, supervisor, expectations, etc. and our Dept Manager brought it up very nicely saying (not verbatum), "Although I really like your perfume I DO find it very over-powering and it's causing headaches. I am asking you to please use it less before you come into the office. Since our quarters are quite small we all need to respect others sensitivities to certain things."
At first the employee was not too happy stating that she really didn't wear much at all (she seemed a bit offended) and our Manager said, "That might be the case, but the amount you currently wear is too much for me and some others to handle so we need you to cut down."
And it worked - I don't think she wears any perfume at all anymore from what I can tell. It wasn't the intent to have her not wear anything, but we're not all suffocating from the over use anymore! Since there are only 6 of us in the office we felt it best to just address her directly.