In New York, you MUST file your return as joint for state purposes, even though the status is not recognized for federal return. The new law applies to tax years starting from 2011, so no retro-amending prior years’ returns.
There are different rules for losses/gains: capital gains, sale of personal residence and etc, so be careful, and do research when preparing the returns.
If you are confused – ask here or consult a professional. Don’t do this yourself – you can miss out on benefits – so in the end you lose…