Jonathan,
3 that come quickly to mind...
1) The Tom Fazio designed Wachesaw Plantation (SC) takes you past an old slave cemetery between the 15th green and 16th tee. It is really quite chilling and well-preserved.
2) The new Jack Nicklaus course at Bayside (DE) passes an old church graveyard between the 7th and 8th holes.
3) The Four Seasons GC in Exeter PA (northeast, has a large graveyard that serves as OB left on the 1st and 12th holes.
4) About a mile from where I sit in Horsham, PA, the Twining Valley GC, circa 1931, runs adjacent to a cemetery on the uphill 11th par three.