Overall, I have to say the Toyota Land Cruiser, (not including Prado versions) is the best choice. It's first in reliability and toughness, and second only to Land Rover for parts availibility throughout Africa.
A not too distant second choice is in fact the Land Rover, Defender and Range Rover models, though definitely not the smaller SUV's like freelander. While Landies fall behind in the reliability category, they are solidly built vehicles and older models especially are known for easy maintenance. The classic Defender takes the lead for adaptability and options. Similar to Jeep TJ's, they are a joy to toy and tinker with with and have cool options like foldable windscreens and removable hard tops. One disadvantage is comfort. Although major improvements have come with newer models, Landies are traditionally designed as tough, no frills military type vehicles.
A not-too-distant third and lesser considered SUV option is the Nissan Patrol, or similar 4X4's. Similar in size and shape, they have an advantage over Land Rover for reliability. Parts are generally available throughout Africa, though a distant third to the LR and LC. Price wise, you get bang for your buck with the Patrol. Slightly more affordable than Cruisers, here in Morocco anyway, they are in the price range of Land Rovers and older models tend to have more perks like AC and comfortable seats.
My fourth option, and I know I'm stretching out on a limb here, is a Beach Buggy, prefferably with big tyres all around to increase clearance. Light weight bodies, easier than any other vehicle to work on, (and they will definitely need maintenance), based on widely available and little changing VW Beetle, they will be stressful, but very rewarding to take through Africa. The engines are tough, your biggest concern will probably be the wiring and nuts and bolts. Learning a thing or two about cars is nice, if not, a VW maintenance book and a list of parts to take can help get you through. Some more obscure parts you might want to bring along are: a brake hose; a couple brake nipples; a couple boot seals and the kit of oil seals including the safety pin to lock the rear brake drum bolt in place; a small box of different sized nuts and bolts and washers; a few metres of basic wire and a few wire heads; a tyre sealing kit and two levers to help remove the tubes; a spare accelerator cable. It's also a good idea to have a big wrench to take off the bolts which hold the rear brake drums in place.
The car to definitely not take are Jeeps. While certainly intrepid and tough, unless you are in a convoy with lots of spare parts, you aren't going to find much in Africa. In fact, for 4X4's, any brand aside from Toyota, Land Rover, and Nissan should probably not be considered. Mitsubishi seems to be making inroads of late, but are not of the same quality and toughness.