Oooh, that was the best holiday we ever had!
Yes to Cheetah Outreach. They're one of the less awful animal-tourist-interaction places because they do actually do important conservation work with LGDs.
Drakenstein Lion Sanctuary is another good one. If you can, you should stay in one of their tents over night. It was the most memorable night of my life.
The Cape of Good Hope is amazing.
We liked Cape Agulhas, where the Indian Ocean meets the Atlantic. It was only a quick stopover, but interesting.
Hermanus to see whales is a must-do.
We stayed in a hostel in Mossel Bay that was a renovated train parked on the beach. It was cheap as chips and very memorable, plus breakfast on the deck overlooking the Indian Ocean, and then walking down the beach into it, was phenomenal. Also in Mossel Bay is an aquarium where you can swim with smooth hound sharks, if the cold water doesn't kill you.
I don't know how far you're going but Addo Elephant National Park was a great beginner safari experience. We saw all sorts, and rather memorably smelled a ripe lion kill. It's funny what sticks with you!
I've just remembered scootering down Table Mountain - that was fun (and terrifying!).
Knysna Elephant park has rooms attached to the elephants' boma (where they sleep overnight); you can stay there overnight, and curl up under blankets on couches overlooking the ellies before bed, watching, listening to and smelling them eat, interact, play and sleep.
Those were the main highlights of our three weeks, I think.