Ok I am probably the last one any of you want to hear from right now, but I am a white South African (though I don't think that should matter), and this debate as to who is better than who is kinda pointless as we tend to compare ones strengths to another weakness. South Africa may be stronger in terms of hardware and technology making it better at conventional warfare, but when did we last have conventional war in African, On the other side, Nigeria has a lot more experience than we do dealing with rebel armies in the African situation however if it came time to invade another country a knowledge as to how to defeat a rebel army wouldn't be as useful as knowledge in conventional warfare, so each country has its strengths where it out does the other, it doesn't matter how many submarines or fighter jets South Africa cause they wont be able to remove a rebel army, you need experienced soldiers, and yet in conventional warfare it doesn't matter how many troops Nigeria has because he who controls the skies and navel trade routes runs the game.

Looking at Military strength is a very poor way of determine a countries ability to make war, a countries army is only as good as its logistical arm will allow it, even the most up to date tank is useless when it runs out of full and ammunition, and at the same time you need a economy to support the logistics. An example of that is Zimbabwe launching a large military campaign into Congo, sure they drove the rebels back, but at the cost of their economy (sure other factors made the situation worse, but the fact remains, war bankrupts countries)

This whole dispute as to who can defeat who is kinda pointless, South Africa cant conquer Nigeria even in our wildest dreams, and Nigeria can't touch us, its a simple logistical problem, the South African army just doesn't have the man power to control a country the size of Nigeria if they don't want us there, and Nigeria who may (and that is a very small chance) have the numbers to hold South Africa have no way of getting their troops to South Africa and then sustaining them once they are there. The closest either side could come to a victory in such a situation would be if South Africa used its submarines and more advanced navel ships to blockade the Nigerian ports, stopping oil exports and there by crippling the Nigerian economy and then hold a siege on the economy till the Nigerian government surrender, but other than that, any attempt by us to land boots on the ground would be as suicidal and any attempt for Nigeria to invade south Africa either via a long distance land run through a number of other African countries or via a amphibious landing assault would be equally suicidal

As for the general question as to which country in Africa has the strongest army, I wont hazard a guess, I think the other options laid forward thus far are good enough indications. Hope my post hasn't offended anyone.