Having just returned from a trip to South Africa, I had to fly from Cape Town to Johannesburg, and I chose to fly with Kulula (www.kulula.com). If you do not know about regional flights like Kulula, I would suggest you click here to read more about it.
Although Travel Butlers do not at the moment book any flights, we often recommend this airline to our customers if their itinerary includes a domestic / internal flight. The prices are generally very good, in fact, I would go as far to say they offer some of the lowest fares around.
They are absolutely ideal for flights between Johannesburg and Cape Town, and also from either of these hub cities onto George, Port Elizabeth and Durban.
I personally had no complaints whatsoever with the check in service when I arrived at Cape Town (the only slight irritation was that the flight I was booked onto was a co-share with BA, and the main flight board showed the BA flight number only, rather than rotating with the Kulula flight number , which did throw me into a mild panic for about 5 minutes until I found someone at the Kulula desk who assured me that my flight WAS still departing !!). There was sufficient legroom in the plane itself, and the service on board was pleasant and efficient.