You can still file a joint return even though your spouse is incarcerated. You need to get your spouse's consent to filing jointly. I would suggest that you himsign the return or a power of attorney authorizing you to sign for him and file a joint tax return. You can even have him sign on the tax return if that is possible.
Let me know if you have any question.
Please note: This advice is provided with the understanding that all the relevant facts have been provided by you. Any change in facts might affect the advice given and hence may not be relied on in such cases. Nothing contained in this reply was intended or written to be used, can be used by any taxpayer, or may be relied upon or used by any taxpayer for the purposes of avoiding penalties that may be imposed on the taxpayer under the Internal Revenue Code of 1986, as amended.