Don't overlook the good ol' nighttime surface attack...at least on the unmodded game. Gotta be a good judge of the light and such, but if the conditions are right, I've made it inside a convoy more than once.
If there's no escort bringing up the rear, for example, you can sometimes creep up on the convoy from behind, fire off a spread of fish, then run like hell, with the convoy between you and the DD's.
Submerged attacks, I tend to use Warhawk's method. Additionally, if you're playing on manual targetting, I find it helps to get so close to a target that doing all the data gathering stuff is unneccesary.
