What is the difference? Which one is good for which.

It depends on the length of the transom on the boat u have. If the distance from the top of the transom to the Keel is 15 inches, then u need a short shaft outboard. If this distance is 20 inches, then u need a long shaft. For small fishing boats, many people prefer a long shaft, since it provides a little more freeboard before waves splash over the stern.

If u try to use a short shaft motor on a long shaft boat, the water intakes may not be completely submerged & the engine could overheat, or the prop might not be deep enough in the water.

l agree with 40something. l will just add, do not put a long shaft motor on a short shaft boat either (without a bracket or jackplate to raise it) -- it will never perform up to its potential; that much motor in the water adds drag, slows it down.