I have a business outside of my day job - Income Tax prep - so I asked the lead attorney at Iowa State Center for Ag Law and Taxation (Roger McEowen) for his take on this issue - with the following reply:
A website toward the lower half of this e-mail will assist in identifying which states have adopted same sex marriage, community property, recognized civil unions, registered domestic partnerships or other legal relationships. The “Windsor” decision only impacts the “same sex marriage” union. Per Revenue Ruling 2013-17, for federal tax purposes, the IRS adopts a general rule recognizing a marriage of same sex individuals that was validly entered into in a state whose laws authorize the marriage of two individuals of the same sex even if the married couple is domiciled in a state that does not recognize the validity of the same sex marriage.
You stated your payroll encompasses 24 states, so regardless of whether the state recognizes same sex marriage or not the federal treatment will be the same as long as it is a valid marriage. Pre-tax basis for federal purposes is allowed.
Each state tax situation will need to be analyzed to determine how benefits will be impacted at the state level. At this time, IRS has only been able to identify which states recognize and allow “same sex” marriage and has not researched further how each individual state will be addressing the issue you have presented.
I was able to find a few resources for Minnesota, Rhode Island, Wisconsin, New York and New Jersey, as noted below.
States Respond to IRS Same-Sex Marriage Guidance
In response to the IRS (Rev. Rul. 2013-17), Minnesota, Rhode Island, and Wisconsin have issued guidance regarding the tax treatment of same-sex married couples. A control and click will link you to guidance provided.
Map by State
New York http://www.mondaq.com/unitedstates/x/143456/New+York+State+Issues+Tax+Guidance+On+SameSex+Marriage+And+Employee+Benefits