I think ancestral citruses (not the crosses) are the primary exception, as well as a few citrus hybrids which create clone seeds asexually.

> Outside of Granny Smith apples the ones you eat are mostly the results of mutations in the grown plants that we cut off and graft.

Honeycrisp is a chance seedling, though it stems from a horticultural crossbreeding effort it was grown from seed. And commercially useful sport mutations tend to come from popular chance seedlings to start with, since it is necessarily a more limited evolution of the basal cultivar, which needs to exist and in sufficient quantity that you’ll roll out useful mutations eventually (also useful is in the eye of the beholder as we can see with the red so-called delicious).