From Zelda Legends Wiki
Blue Bubbles are skull-looking enemies with blue smoke/fire covering them.
Ocarina of Time
Blue Bubbles are skull-looking enemies lurking inside the Forest Temple. The best way to shoot a Blue Bubble is to shoot them at Hookshot, the fire will disappear and the skull will fall to the ground.
The Wind Waker
The bubble has blue smoke instead of fire floating around it. If Link touches the smoke, he is not able to use any items. The smoke will disappear after some time has passed. The bubbles can be defeated by shooting an arrow to it's head.
--Gameboy 12:40, 23 July 2007 (EDT)