OK, I haven't dove all the places yet, but I can give you a starting point.
1. Aliwal Shoal (Raggies, bull, tiger sharks, mantas, etc.)
Diving Aliwal Shoal
2. Protea Banks (much the same as Aliwal)
http://www.africandiveadventures.co.za/protea.html
3. Sodwana Bay (sharks, mantas, whale sharks, nudibranches, EVERYTHING!!!) I rate Sodwana as best diving spot in South Africa, and recommend to dive through ReefTeach -
Scuba Diving South Africa Sodwana bay - Dive Sodwana Bay
4. Mozambique (whale sharks, turtles, mantas, etc.) - Also many different places to visit, starting at Ponta do Ouro in the south to Pemba in the north. Check out Ponta, Inhambane, Bazaruto, Pemba
mozambique map
I still want to dive "Bassas da India" which is only accesible via live-aboard in the Mozambique Channel.
Bassas da India - Wikipedia, the free encyclopedia
Map of scuba dive sites in South Africa and Mozambique