Actually if you are separated only the custodial parent would be counted on the FAFSA. This excerpt from the studentaid.ed.gov website:
"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."
Here is a link Completing the FAFSA 2010-2011/The Application Questions(59-93)
Of course some schools may consider the noncustodial parent through other means (Non-Custodial CSS Profile and/or their own institutional forms)