Maritime surveillance aircraft routinely shut an engine down since they are operating on endurance, not range. They sometimes cage two engines. They even used to do this on piston transport based platforms: the Canadian Argus comes to mind, I always wondered about restarting cold-soaked radials after a long loiter in February.
Other types from the cold war would routinely shut down some propulsion: The P-2V and the B-36 come immediately to mind.
From memory, a 747-400 burns 8% more fuel on three engines, but in some cases less than flight plan with two shut down.