In our Goju ryu class we have the bunkai also for the application of the moves in kata.We also have kiso kumite to use as a way to flow a series of techniqes at each belt level.
The last part of each class we work on self-defence that might not be in the kata exactly,but work on scenerios and possible counters.
I find that while the kata moves at first glance don't look applicable in SD, I had to change my mind on this as their worth becomes more and more evident. A perfect example of this is Saifa kata.At first it seemed to be a flowing artsy kata with not much "bite" to it. This was my narrow mind evaluating a kata before really learning it.Now I find techniques all the time from Saifa that would defend you well on the street.