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Generally, for most states, you need to file the state return the same manner in which you file the federal. Most states however have an exception to this when the spouses are residents of different states. I could give you the exact answer if I knew which two states you and your wife live in.
I live in WV, she lives in MD. She has no wage or salary income (only a modest Sched C loss), and there was no witholding in MD. I think the right answer is to file jointly as WV resident and don't even file in MD at all. Sound right?
For WV, you have the option of filing jointly or separately for the state return. If you wife has only a loss, it will most likely benefit you to file a joint WV return.
See page 5: http://www.state.wv.us/taxrev/forms/2010/it140.booklet.pdfY
Your wife is permitted to file a separate MD return, in order to find out if she must file, she should see the chart in the booklet. If she has no other income then a loss, she is not required to file:
pages 5,6,7: http://forms.marylandtaxes.com/current_forms/resident_booklet.pdf