In "The Magnificent Seven" Dean and Sam are called to Lincoln, Nebraska by Bobby. He has uncovered what he thinks is a demonic indicator and has called the boys into assist him in cleaning it up. They discover a family, dead in front of the their tv, with no obvious cause.
Lincoln was also prominent in another pivotal SPN episodes Devil's Trap. Meg Masters has John Winchester come to a warehouse in Lincoln, Nebraska, after killing Caleb in the city.