Why did some aircraft use hand-crank instead of gravity for alternate gear extension?
They had to manually crank down the gear because the electric system was damaged. 

"As the B-17 limps closer to base, Dearborn orders the landing gear dropped. Only one wheel descends due to electrical failure caused by battle damage, but the crew are able to manually lower the malfunctioning wheel just before landing." 

Free fall only works for hydraulic powered landing gear systems. The B-17 uses an electrically driven motor to raise and lower the gear. 

Not all hydraulic landing gear can free fall. PBY-5A's have hydraulic gear and emergency gear extension used a backup hydraulic pump. Additionally you could manually break the up locks and then manually push the gear to the locked position. 

I bet many other WWII era aircraft with hydraulic gear were similar. Free falling hydraulic gear probably came much later.