In what was one of the two most anticipated cases in the Supreme Court's docket this year (and arguably in many years), the Supreme Court ruled in United States v. Windsor that the federal Defense of Marriage Act (DOMA) was unconstitutional as it violated the Constitution's Equal Protection and Due Process Clauses.
DOMA had two operative sections: one was the definition of marriage as between that of one man and one woman, and the other granting states the right to not recognize a legal same-sex marriage performed in another state. At issue in Windsor was only the definition section; the other section is still valid law. This means that while states are still free to accept or reject same-sex marriage-to rule otherwise would have been so controversial that many argue that's why the Court didn't rule on it-the federal government must recognize legal same-sex marriages if the state in which the couple reside also recognizes the marriage.
Of course the IRS and U.S. tax code come into play. In fact, the entire case in Windsor was around the surviving spouse being forced to pay federal estate taxes despite being legally married in the state in which they resided because DOMA prevented the federal government from recognizing their marriage. Due to this ruling, not only is Windsor entitled to a refund of the payment she made (calculated to be around $638,000 plus interest), but so are any same-sex couple who couldn't take advantage of tax deductions or exemptions that they otherwise could have had their marriage been recognized.
This is because cases that revolve around issues of constitutional law have rulings that apply retroactively. But the statutes of limitations that indicate how long one has to file for a refund remain unaffected. Therefore only those who have been impacted in the last 2-3 years are the ones who can file for a refund, but they must do so quickly. Unless Congress acts to grant these individuals a longer time, the statute of limitations may prevent them from recouping taxes they were forced to pay even if the Supreme Court has vindicated them.