Answer by Wray Rives:
The answer is yes a same sex couple who are legally married in a state or foreign jurisdiction that allows same sex marriage can file an amended return to file as married filing jointly (MFJ) or married filing separate (MFS) as long as the 3 year statute of limitations has not passed on filing an amended return, but it is actually a little more complicated than that and some same sex couples may actually have to pay more in total taxes than they did filing as two single individuals.
Same sex couples (when I say same sex couples here I mean ones that are legally married) who filed their 2012 tax returns after September 16, 2013, are required to file an amended return if they did not file as MFJ or MFS for 2012.
For tax years 2013 and going forward same sex couples are required to file as either MFJ or MFS. If they did not, they must go back and file an amended return for 2013.
For returns filed prior to September 16, 2013, same sex couples have the option, but are not required to file an amended return filing as MFJ or MFS.