You would use "had been waiting" if you were referring to that in relationship to some other past event that took place after that. Otherwise, the simple past is better. I had been waiting for you for three hours before you called me.
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You would use "had been waiting" if you were referring to that in relationship to some other past event that took place after that. Otherwise, the simple past is better.
I had been waiting for you for three hours before you called me. (I had been waiting before the other event, that you called me.)
I was waiting for you for three hours. (I say that when you arrive.)