The main ones I know of relate to tetrapod limb development.
1) The webbing between the fingers - in species where it is absent - is eliminated by apoptosis. These are the interdigital "necrotic" zones.
2) There are 3 "necrotic" zones (anterior, posterior, and interior) in the limbs where apoptosis occurs.
There are clearly many more examples than that; I just don't know them off the top of my head.
PS: They were named necrotic zones before apoptosis was known, or else they would not have been given the incorrect name "necrotic".