Despite the fact that you were not living together the last few days of the year, the IRS maintains that as long as you were still married you have the option to file married filing jointly. You can refer to IRS Publication 504 for further details. Please click the link below to access this IRS publication.
Publication 504 (2009), Divorced or Separated Individuals
But, keep one thing in mind is that the IRS tax code states "that if you and your spouse file separate returns and one of you itemizes deductions, the other spouse will have a standard deduction of zero."
Also, some tax credits cannot be used at all if you file separately such as the the child and dependent care credit, the hope and lifetime learning credits, and adoption expense credit.
Furthermore, if you live in community property states including Arizona, California, Idaho, Louisiana, Nevada, New Mexico, Texas, Washington or Wisconsin, you may need to consult with a CPA or a tax professional because the tax rules about filing married filing separate returns can be very complicated.