The ship graveyard is a location which features in Uncharted 3: Drake's Deception. It is located somewhere off the coast of Yemen, and consists of several ruined ships, pontoons, and a handful of buildings. It was later developed into a multiplayer map: Graveyard.
Nathan Drake was brought to the graveyard after being abducted by Rameses and his pirates. The entire graveyard was controlled by them, and they were possibly using it as their base of operations. On the outer edge of the graveyard Rameses kept his cruise ship, The Seaward.
The graveyard only appears in Uncharted 3: Drake's Deception, in the following chapters: