Book Far in Advance
Airlines schedule their flights 330 days ahead. So ideally, you can begin to look for mileage options around this time. Unfortunately, the airlines will not always allow you to use your points or miles this far in advance. They like to wait and see how the full fare tickets are selling, before they offer "saver pass" seats. Saver pass rewards are very much capacity controlled. And unless you have a vast amount of miles, you ideally want to wait for the best mileage award deals since a typical round trip to Africa (from the US) will cost a minimum of 80,000 miles per ticket.
Get Familiar With Alliance Agreements
It is much nicer to fly to Africa direct if possible, than endure a layover in Europe or the Middle East. Unfortunately the list of airlines that fly direct is slim from the US. They include Royal Air Moroc, Air Egypt, Delta, United, South African Airways and Ethiopian Airlines. Check with the lists of alliance partners to see if one of these airlines will accept your miles, before trying anything else. One of the most useful airlines groups to collect miles on is Star Alliance. If you have miles with United/Continental or US Air you can possibly use them for direct flights to Africa on South African Airways, Ethiopian Airlines, and EgyptAir. Other airlines in this group offer many direct flights from Europe to Africa, they include Lufthansa (via Frankfurt), TAP (Portugal) (via Lisbon) and Swissair (via Geneva).
The Stopover in Europe
European stopovers may make it easier to use your miles simply because there are lots of flights available so more inventory for airlines to get rid of. But the layovers can be lengthy and the various taxes added can add a significant price tag to your "free ticket". In some cases stopping in Europe adds a day of travel, that is really better spent on vacation than in an airline cabin. There are destinations in Africa that are only accessible via Europe, so you don't always have much choice. But check South African Airways and Ethiopian for some good regional connections. If you do end up flying to Africa via Europe, then think ex-colonies to get the most flight options. For example, the most frequent flights to Namibia leave from Frankfurt. If you are looking for a flight to a West African country, use Paris as your hub. For East and Southern Africa most flights will go in and out of London.
Don't Forget the Middle East
Emirates has an extensive network in Africa with good layover times (often better than Europe). Emirates however does not partner with many airlines so unless you fly to Africa frequently and accrue miles with them directly, it may be difficult to use reward points. However, they do have a great network along with excellent service, and fly to the Seychelles, Nairobi, Mauritius, Uganda, Johannesburg, Tanzania and more. Qatar Airways is also a good option, with services to Kigali, Johannesburg, Mombasa, Zanzibar, Alexandria, Entebbe, Casablanca, Lagos, Nairobi and more.
Know Your African Geography
Using miles to get close to your final destination in Africa may not be a great money saver. Regional flights in Africa do not come cheap, and local airlines can be a little unreliable in sticking to their timetables. You don't want to miss half your safari because you were so intent on saving some money getting there. African countries are large, so getting to a capital does not necessarily mean the same thing as getting to your ideal destination. If you've planned a safari in Tanzania's Serengeti and managed to use your miles to fly into Dar es Salaam, you may be shocked to hear you are still a 9 hour bus ride away.
Best Regional Hubs to Fly To
There are some African cities that are better to fly into than others if you want to use miles. They have a reasonable network of regional flights to get you to your final destination. But beware that many African capitals are quite expensive, so limit your layover time if possible. If you end up spending an extra few nights because of a timetable change, you'll negate any savings you gained using your miles. Top choices for regional air travel hubs include: Johannesburg (for Southern Africa), Nairobi (for East Africa), Dakar (for West Africa), Casablanca (for West Africa), Cairo (for East and West Africa) and Addis Ababa (for East Africa).
And if You Don't Succeed...
I have rarely been successful in using airline miles to get to Africa. In the end I just look for the best deal I can find on a flight that is as direct as possible. Then I use the miles I accrue from these flights to save on family travel to Europe or flights within the US.
If you don't fly a lot, you may want to earn airlines miles through a credit card, hopefully you'll spend enough to get you to Africa! About.com's Budget Travel guide has some good tips on finding The Best Air Miles Credit Card.