These couples are filing amended federal tax returns listing themselves as "married and filing jointly". The Internal Revenue Code allows protective claims and the returns will be put on hold pending the outcome of, in this case, the Supreme Court's decision in those two cases.
The Defense of Marriage Act (DOMA) prohibits the feds from recognizing same-sex marriages. This means lesbian and gay married couples cannot file as married on their tax returns. They must file as "single". However, since they are legally married there is a concern about the "under penalty of perjury" provision when they sign their returns. It's a conundrum for them--they aren't single, except where the feds are concerned because of DOMA.
This is where the protective claims come into play. Look at IRS Pub 556 for additional information on how to file and talk to your tax preparer. There is a 3-year look back period for filing an amended return. You'll be able to go back to tax year 2009.
Protective claims are often based on pending court cases, like Windsor. It may be worthwhile to checkin into whether you are eligible to file a protective claim and whether it will do you any good. In some cases, a married lesbian/gay couple may be entitled to a refund.
No guarantees but it should be a consideration.