This is a great thread.
I loved "bible stories" as a kid and often asked my Mom to tell them. Unfortunately for her, I asked her questions... lots of them... expecting her to make everything make sense. She couldn't.
One that baffled me the most was Abraham bargaining with Jah for Lot's life. Wait, Jehovah is all-knowing, right? Why didn't he know about Lot and his family in Sodom and Gomorrah? Well, he did know, right? Well then why did Abraham have to convince him? Was Jehovah just messin' with him? Any way you slice that one, it's pretty disconcerting (and that's before you even get to the crazed ugliness in the Lot story.)
New International Version (NIV)
Abraham Pleads for Sodom
22 The men turned away and went toward Sodom, but Abraham remained standing before the Lord . [b] 23 Then Abraham approached him and said: “Will you sweep away the righteous with the wicked? 24 What if there are fifty righteous people in the city? Will you really sweep it away and not spare [c] the place for the sake of the fifty righteous people in it? 25 Far be it from you to do such a thing—to kill the righteous with the wicked, treating the righteous and the wicked alike. Far be it from you! Will not the Judge of all the earth do right?”
26 The Lord said, “If I find fifty righteous people in the city of Sodom, I will spare the whole place for their sake.”
27 Then Abraham spoke up again: “Now that I have been so bold as to speak to the Lord, though I am nothing but dust and ashes, 28 what if the number of the righteous is five less than fifty? Will you destroy the whole city for lack of five people?”
“If I find forty-five there,” he said, “I will not destroy it.”
29 Once again he spoke to him, “What if only forty are found there?”
He said, “For the sake of forty, I will not do it.”
30 Then he said, “May the Lord not be angry, but let me speak. What if only thirty can be found there?”
He answered, “I will not do it if I find thirty there.”
31 Abraham said, “Now that I have been so bold as to speak to the Lord, what if only twenty can be found there?”
He said, “For the sake of twenty, I will not destroy it.”
32 Then he said, “May the Lord not be angry, but let me speak just once more. What if only ten can be found there?”
He answered, “For the sake of ten, I will not destroy it.”
33 When the Lord had finished speaking with Abraham, he left, and Abraham returned home.
I also had several things about the creation story that bugged me endlessly, but that one can get pretty long-winded.