Here are a few possibilities that I came across that seemed interesting, as well as within our travel radius...
Buffalo, NE (Custer County)
2WD roads HWY 21 North of Lexington ~ 13 miles; turn west (the road will wind south)
Kinney, NE (Gage county)
4WD roads 8 miles East of Wymore; at the base of Kinney Hill, go south 1/4 mile. Town sat just north of the bluff at the turn in the road.
Supposed to have been a rough town; in the 30's, a shootout caused the deaths of some good and bad guys (lore has it that some of the stolen booty was never recovered).
Spring Ranch, NE (Clay county)
2WD roads Bridge, cemetery, abandoned hotel
Town destroyed by tornado in the 1900's
Lore: "two people supposedly hung under a bridge that is now said to be haunted".
St. Deroin (Nemaha county)
2WD roads 10 miles S of Brownville on HWY 67, then 5 miles E on 64; in Indian Cave State Park.
Cemetery, Steamboat landing on MS river in the early 1900's.
Arborville, NE (York County)
2WD roads West and North of Bradshaw (~9 miles) NW corner of York county
"Church, Cemetery, a few houses" I do not know if they are inhabited
Minersville, NE (Otoe County)
4WD roads Coal shafts (bluffs above the town); cave-ins/deaths Downtown area uninhabited Cemetery lost? Used to ferry people across the river.
Oak Grove, NE
2WD roads 2 miles Southeast of Oak South side of the Little Blue River Oregon trail markers Old Mill, 2 historical markers, 2 homes, cemetery
Supposedly, there are tunnels that run under the 'main street' area of town, and they are haunted.