You have to clarify exactly what you mean by "separated." If you were "legally separated from your spouse under a divorce or separate maintenance decree" you are considered unmarried. In that case you cannot file as married filing jointly, or as married filing separately. You have to file as single unless you meet the requirements to file as head of household. The exact nature of your separation is a legal question. Not all states have legal separation. If you're not sure, consult a lawyer.
If you were not "legally separated from your spouse under a divorce or separate maintenance decree" then you are still considered married. In that case you have to file as either married filing jointly or married filing separately. Be sure to coordinate with your spouse's executor. If you do not file jointly the executor will have to file a tax return for your spouse as married filing separately. If you do file jointly, the executor cannot file a separate return for your spouse. The executor also has the option to not allow you to file jointly, even if you want to.
(Since you were separated in some fashion, I assume that you are not your spouse's executor. But if you are the executor, then you are responsible for filing your spouse's final tax return, either separately or jointly with yourself.)
