In SH3 I Only limit myself to using one torpedo to one ship, and only ships 4000+ tons. If called for I use a second but normally I will wait around for up to 12 hours to wait and see if she sinks. For merchants under 4000 ton I use the 105mm and the 37mm. Also I only take shots on moving targets if they are within 800m and the AOB is close to either 270 or 90. In response to Iranon's post stating that ships with an AOB of 0 or 180 have no viable solution, that is wrong. In order to hit a target with an AOB of wither 0 or 180 you slip in behind or in front of the target set range slightly shorter than needed (to make up for the fact the ship is closing fast) set you AOB accordingly then fire. Speed is irrelevant in this case because the target is on the same course. I disable many ships with 180 AOB shots, as the torpedo almost always destroys the propulsion systems.
Even a battleship can be sunk with just one torpedo:
Both the Southhamptons went under in one torpedo, that London class took three.
When attacking merchants, follow everyones advice and aim by the smokestack or just in front of the bridge. For naval ships, aim underneath the main guns. These are the ammunition stores.
When I use keel shots I aim for the center of the ship and set them just under the draft.
In the Type IX it is usually fairly common for me to pull in 60000ton patrols following these guidelines.