Tax advice for Residence in multiple states.
You would have 2 W-2's one showing State wages for WI and the other showing wages in PA. In fact, if you were to examine your W-2's, you will see one copy that indicates an amount for PA State Wages and another copy that indicates an amount for WI wages. Therefore, you would be required to file a multi-state tax return, one for WI and one for PA.
You are now a resident of PA it seems, and so PA would be the resident state. However, it seems that you might not have moved to PA at the beginning of the year, so you indicate on the PA and WI form when you were a resident of that state. Clearly, it seems that your wife has abandoned WI and moved permanently to PA. In her case as well you would indicate that she is not a resident of WI, but a resident of PA.
You would have to file a Non-Resident Form for WI State if you choose PA as a permanent residency, and a Part Year Resident Form for PA. I think since your wife has left WI permanently it might be prudent to elect PA residency.
How should you file the returns?
With respect to filing the Federal tax return, you can always file a joint tax return. As far as the State tax returns are concerned, you would file a joint tax return but would show on the WI State with your wife as a current non-resident, but a part-year resident. On the PA joint tax return, you would show both of you as a part-year resident.
Clearly, this return is very complicated and I would really recommend that you seek the advice of a CPA or a expert tax advisor who is an expert in the field in of multi-state tax returns.