I'm aware of Atlas Games' Nyambe, and I read the Kindred of the Ebony Kingdom sourcebook that White Wolf released for Vampire some years back. Which other books treat the area well, or at least as a good setting for adventures?
There's a new supplement from Paizo for the Mwangi Expanse, the Africa of Golarion, called "Heart of the Jungle" in support of their new Mwangi-based Pathfinder adventure path, Serpent's Skull. I'm using it and Nyambe to do some African adventuring of my own.
Well, there's the Dark Continent: Adventure & Exploration in Darkest Africa rpg; however, I'm not sure that it's still in print. Chaosium used to sell copies of this game through their online store, but I'm not sure they still have any -- this may have become a collectible item. The tone of the game may not suit your purposes: it's firmly a pulp-era "big white hunter" colonial exploration/exploitation type of setting, with the focus on exploring the "dark continent". It is sub-Saharan in focus, though, and might have setting material you could use.
Notice, also, that RPGGeek has a geek-list that covers this question (although it doesn't ask for good treatments, just asks for games that have an African theme.
Nyambe for D&D3.X is pan-african, but ignoring the Copts and Greeks (Egyptians both...)
South of the Sun for Ars Magica is a setting book for Africa of legend; it's not realistic at all, and focuses on an odd mix of pagan egypt and Prester John's Christian Kingdom in the South.
Both are, as far as I know, out of print.
Aesheba: Greek Africa, is a good 80s supplement by Frank Mentzer and Bob Blake, dealing with a generic African-type continent that can be placed in any RPG world. There are many Egyptian and Greek type civilizations on this "lost" continent, new monsters, spells, etc and as a setting it can give plenty of good ideas. This might not be exactly what you are looking for because this is an Africa where Greek explorers have made their mark on the continent by colonizing several northern stretches; however african style "lost" cities and civilizations dot the inner continent (which is more of a fantasy style Africa since there is no Nile river here so races can easily spread throughout the continent). The material does focus more on the "explorers" point of view than any native peoples, but you might be able to salvage a few good ideas from the book and I notice it doesn't seem to ever sell for very much on the secondary market (making it cheap to pick up).
I run an "African Style" campaign and some of the best inspiration I have come across are in real-life histories of the region. Here are a few books I read and recommend for some insight into real-life African history, which can be used to set up your own jungle/african like setting:
The Scramble for Africa (Deals with the conquest and exploitation of the continent in the late 19th century through early 20th century);
Travels in the Interior of Africa by Mungo Park (the first white explorer to penetrate the interior and map the Niger river, very interesting);
Africa: A Biography of the Continent (perhaps a bit too real life and topical for some, still very informative)
Spears of the Dawn is a promising candidate. I've read the Beta Version that was released to Kickstarter backers (it's been fully funded and then some), and it appears to meet all my qualifications.
It's rather specific as well as set in the 1920s, but the CoC sourcebook Secrets of Kenya probably has some good hooks for adventures (I don't own a copy, so can't comment directly). You can see a preview of the content (first 14pp) here
There's a supplement for Ars Magica called South of the Sun that deals with Prester John and "...a medieval vision of Mythic Africa".
I always enjoyed Ars Magica - I have the three latest editions on my shelf. But I never picked up this particular book.
Edit - Whoops! Didn't see Aramis' post about this book above until after I had finished it!
Punaiset hiekat - Somalia roolipeleissä treats Somalia in a system-neutral manner, in Finnish. It discusses several different genres of play. More information (in Finnish) over here. In particular, there are example scenarios and discussion of Somalia as an adventure setting, as well as discussion of the culture. The author has researched the setting deeply and gives a good view of the cultural setting, which is quite interesting.
I think that Conan RPG is also providing a good low fantasy African themed RPG. As you can see the world map is quite looking like Africa:
Some supplements of this game should be more suited to what you are looking for, like this one:tales_of_the_black_kingdoms