A bunker, in
military terms, is a structure that is at least partially below
ground level and is
fortified to resist
weapons fire or other catastrophic events like nearby
explosions. Generally, they resemble roofed-over holes in the ground with slits which allow the occupants to look out and if necessary fire upon objects/people/vehicles moving nearby.
They aren't always used as active defense strongpoints, though; typically, for example, ammunition is stored in low underground buildings (bunkers). This is so that it is protected from attack, but also so that in the event some of the ammunition or volatile material (read: gas) explodes, the force of the explosion is directed upwards by the walls of the bunker and presents less of a threat to the surrounding storage areas and personnel.
Actually, I just remembered; the term also refers to the compartment of a ship where fuel is stored. It originally referred to the coal storage area on steamers; now, however, it is used to describe liquid fuel storage for the ship and any related systems. Aircraft carriers have jet fuel bunkers, just as oil-fired ships have oil bunkers.
Addendum: baffo informs me that 'bunker' is also used to refer to the fuel used by oil-fired ships itself; a tar-like substance, it must be heated to approximately 100 degress Celsius before it even becomes liquid and can thus be piped and burned. Thanks baffo!