many times a few different methods i typically use are:
possess the big daddy to believe that you're a little sister, then run out of the room, go do a few things, then come back to see another one spawned.
wait for him to go collect the little sister out of the cubby hole, then shoot him once, this will initiate the battle of the big daddys, which is also interesting to watch.
but, if u dont have the time / want to do that, another method i like to use are the proximity mines.
lay down a straight path of 3 or four of them about 8 feet apart, the beauty is, is that he never attacks you unless you attempt to hurt the little sister or attack him.
at which case you have the big daddy lined up on the far side of a few proxy mines, pull out your machine gun, and unload. he'll come runnin at you like abat outta hell, blowing up all the mines, and should be pretty much dead by the time he reaches you.