SA295 has been shrouded in mystery but many think the cause was combustion of munitions being transported back to SA from Taiwan, at the time one of SA's only three or so 'friends' in the world. I lost a number of travel industry colleagues on that flight as a group of travel agents on a fam trip were on board.
SA406 was rumoured as sabotage, as someone high profile was on board, off the top of my head I seem to recall it was someone high up in the military.
SA228 was probably primarily caused by a slat retraction error but as always a combination of circumstances. The aircraft was only a few weeks old.
I can't say SAA's pilots were the best in the world as I don't have the experience to validate that statement, but they were bloody good compared to many other airlines I flew on. We were proud of our 'Lugdiens' even if they were a pain in the backside.