This is from the FAFSA faq (08-09):
If your parents are legally separated, the same rules that apply for a divorced couple are used to determine which parent's information must be reported. A couple doesn't have to be legally separated in order to be considered separated for purposes of the FAFSA. The couple may consider themselves informally separated when one of the partners has permanently left the household. If the partners live together, they can't be considered informally separated.
It is a loose interpretation, only you can make the the final decision how you will file.