The Treasury just published updated tax guidelines for same-sex marriages, and the document specifically states that
employees who purchased same-sex spouse health insurance coverage from their employers on an after-tax basis may treat the amounts paid for that coverage as pre-tax and excludable from income.
Individuals who were in same-sex marriages may, but are not required to, file original or amended returns choosing to be treated as married for federal tax purposes for one or more prior tax years still open under the statute of limitations. Refund claims can still be filed for tax years 2010, 2011, and 2012.
Question 10 (Q10) of the IRS FAQ for same-sex couples gives more details:
Generally, a taxpayer may file a claim for refund for three years from the date the return was filed or two years from the date the tax was paid, whichever is later. If an employer provided health coverage for an employee’s same-sex spouse, the employee may claim a refund of income taxes paid on the value of coverage that would have been excluded from income had the employee’s spouse been recognized as the employee’s legal spouse for tax purposes. This claim for a refund generally would be made through the filing of an amended Form 1040.
The document also makes several other points that may or may not be relevant to your specific situation, but they're good to keep in mind. I'll quote most of this verbatim:
All legal same-sex marriages will be recognized for federal tax purposes. If a couple was legally married in a jurisdiction that recognizes their marriage, they will be treated as married regardless of where in the US they live now. However, the ruling does not apply to registered domestic partnerships, civil unions, or similar formal relationships recognized under state law.
Under the ruling, same sex couples will be treated as married for all federal tax purposes, including income and gift and estate taxes. The ruling applies to all federal tax provisions where marriage is a factor, including filing status, claiming personal and dependency exemptions, taking the standard deduction, employee benefits, contributing to an IRA, and claiming the earned income tax credit or child tax credit.
Legally-married same-sex couples generally must file their 2013 federal income tax return using either the “married filing jointly” or “married filing separately” filing status.
These are just the basic guidelines. As always, speak to a tax professional to make sure you file your amended returns correctly. Amended returns aren't anything new to the IRS, but the repeal of DOMA is; it can't hurt to have someone there to represent you to the IRS in case some forms aren't 100% correct.
Furthermore, you'll also want to speak to a tax professional because you may face other financial changes that come with being married too. I don't know if all of those will apply to you, but they're worth understanding just in case. Keith's answer is very thorough, so I won't go into details here.