Cape Town has many township tours available. Most will include the Cape Flats as well as a visit to the District 6 Museum and the unique Malay settlement of Bo Kaap. Tours are offered by Zibonele Tours and Nomvuyos Tours. For more information and tour companies see my guide to Township Tours in Cape Town.
Just outside Johannesburg, Soweto should be part of every traveler's itinerary if you're in the area. There are half or full day tours and if you truly want a full experience you can stay at a local B&B. More than 3.5 million people live in Soweto. It's a vibrant, lively place, as a visit to a local shebeen will prove. For more tours and information see my guide to Soweto Tours.
Durban's townships are also worth a visit and many such tours will provide fascinating insight into Mahatma Gandhi's early life as a lawyer and activist in South Africa. Lynx tours offer a typical half day township tour.
While South Africa's townships are well known, countries with a similar political history, like Namibia, also have townships that are worth visiting. In fact, many African capitals have areas that the tourist may never see, but probably should, since most of the local people live there. Nairobi's Kibera slum is an excellent example.
Image of Soweto; © David Hutchinson