CC - I think this one will have many different opinions.
I will just tell you what the boats around here have.
Covered back deck has about 3 inches clearance between covered deck and prop, about three inches between cage and prop. (Billy Kline built)
Covered back deck has about 2 inches clearance between prop and deck and 4 between prop and cage. (Boyd Stossel built)
Panther (Classic 14' with 350 gearbox) have about 4 inches clearance between prop and transom, and has about 12 inches of a 76 power shift below the back of transom.
Mark's said about 2 inches was fine between rudders and prop, cage alittle more.
If you want I will be around 4 to 6 boats tomorrow and can get measurements. I check if you want, post a note tonight or in the morning.
I agree with Big Daddy. Alittle extra clearance is nice if you are running dry alot. Have watched a few things pass through that clearance unharmed, so the larger the gap is nice (within limits of course).