Since you lived together during part of the last half of the year, you should file as married filing jointly. You just ignore the period of separation and file your joint tax return the same as if you lived together all year. The separation does not affect your taxes.
As I mentioned earlier, if you live in Ohio and both have income, you might find that by filing as married filing separately you save so much on your state tax that it more than compensates for the additional federal tax that you have to pay. The only way to know for sure is to try it both ways and see which works out better. This is because of a quirk in the Ohio state tax law. If you don't live in Ohio, just forget about this and file jointly.
Filing as head of household is not an option in your situation. Your only choices are married filing jointly or married filing separately. As stated earlier, married filing jointly is almost always better.
