Yesterday the Internal Revenue Service issued an important ruling in the wake of the Windsor case in which the Supreme Court ruled that the Defense of Marriage Act was unconstitutional. Specifically the IRS stated that it will recognize all same sex marriages regardless of where the couple was married.
The Supreme Court did not specifically address what would happen if a same sex couple got married in one state and then moved to another state that did not recognize the union. Now it is clear that the IRS will respect the marriage regardless of where the couple moves afterwards.
The IRS also stated that starting with the 2013 tax year, all married couples (same sex or opposite sex) must either file as married or married filing separately. Additionally, same sex married couples may elect to file an amended income tax return for the 2010, 2011, or 2012 calendar years. You should seriously consider amending the return if one spouse worked and the other didn't or if there are other significant tax advantages.
It should be noted that the IRS rules only applies to married couples, not civil unions. New Jersey and two other states currently allow only civil unions. The most likely outcome of this is that the civil union laws will eventually fall by the wayside in favor of same sex marriages as separate is once again inherently unequal.