How do I file my special snowflake taxes?

Not sure about your exact situation, but as a general rule you must file the same way on your state return as you do on your federal return. Exceptions to this are very rare.

I don't know about the OP's situation, and I'm not clear why it would be to her advantage to file her state taxes separately, but married gay couples in California generally file jointly for the state and separately for the Federal tax, so it can be done that direction, anyway.

Thanks, Winnemac! There is indeed a Volunteer Income Tax Assistance site at my university. I'll check them out this week.

Not expert advice, but it seems like it's up to the states whether this is allowed, and I have the Massachusetts tax booklet next to me and just downloaded the Maryland one from http://individuals.marylandtaxes.com/taxforms/11forms.asp#resident. http://www.mass.gov/dor/individuals/filing-and-payment-information/guide-to-personal-income-tax/filing-status.html#Married, and looking at the booklet I don't see anything that contradicts it. It does say clearly that you'll have to file the Massachusetts returns separately. In the Maryland booklet, the chart and instructions under sections 7 and 8 specifically address "Married couples who filed joint federal returns but were domiciled in different states on the last day of the tax year" and "If you and your spouse file a joint federal return but are filing separate Maryland returns" - at a glance it looks like you can do it but there are extra instructions to follow? But probably worth checking out those tax assistance resources to be sure!

Another n that this might be possible, of course with the caveat that you should talk to an accountant and/or the IRS. One year, my husband and I filed our federal taxes jointly and our state returns separately. In the middle of the year, I had moved out of state (NY to MA) for a new job (and got an apartment, car registration, the whole shebang), while he had completed the year in NY (and kept our old apartment, car registration, etc.). The only accurate way to file was for me as part-year in both states, and him full time in NY. To accomplish this though, we did the federal taxes as usual in the joint manner, and filed them that way. Then to complete the NY and MA forms, we also each had to do our federal taxes as though we were filing separately (but we didn't file these mock returns -- they were just for calculations), since each state asks for figures from the federal 1040. It was of course annoyingly extra work, but it ended up getting us a better return, and it was the only way to be honest, so win win. Randomly, another issue came up with my NY return that was unrelated to this whole thing, wherein I ended up on the phone with a NYS DOR guy for a while. He asked me about the unusual joint feb/separate state, but I just said that we had done so because "it was accurate to our situation," and that was sufficient. (the previous comment just came up, so yeah, I agree, it might be state-specific, and I was in the right states....ymmv)

That's very reassuring, Tandem Affinity! "Accurate to our situation" is the perfect way to put it, since we do have combined finances but maintain residences in different states. I was wondering how to deal with the AGI numbers in the state returns, and didn't think about running the numbers separately just for them. I'll report back once I meet with the tax assistance people!