The African continent has a rich and complex history that is only recently being excavated out from under centuries of colonial rule, and integrating this history into our overall understanding of human development in the past seventy thousand years is going to be the work of generations. Even periods as recent as the Middle Ages are only slowly starting to come into focus thanks to the work of the past generation of historians and archeologists.
The most notable feature of African geography is the Sahara to the north, which almost completely cuts off the rest of the continent from trade and migration except by sea, and ocean traffic from Europe and the Middle East presented a considerable challenge up until Early Modern times, although Arab colonization and trade across the Indian Ocean to Africa’s east coast did occur earlier.
On land, the Sahara is a sufficiently impassable barrier that it appears to have dominated early hominid migration out of Africa, with the most recent--and only successful--migration by H. Sapiens (us) having taken place some 50 to 70 thousand years ago across the Bab-el-Mandeb strait at the mouth of the Red Sea, which separates modern Ethiopia from Yemen, and which may have been dry at the time due to the low sea levels attendent upon so much of the world’s water being tied up in glaciers. Other, earlier, migrations of various members of genus homo may have depended on "African Pluvials" (rainy eras) to permit migration down the Nile Valley or across the briefly green desert. Those included some small bands of anatomically modern humans leaving, but so far as we can tell from genetic evidence they all died off.
So sub-Saharan Africa remained relatively inaccessible to the rest of the world until between one and two thousand years ago. There was some contact before that, of course. Romans traded for slaves up the Nile, and the ancient Greek historian Herodotus--whose book, entitled Researches, gives us the word history--described a supposed voyage by Phoenician sailors that circumnavigated Africa (he does not record if any of them were named Phlebas).
Interestingly, we can be fairly sure this Phoenician account is accurate, because Herodotus tells us that the sailors observed the sun on the left hand side at noon as they sailed east around the southern tip of the continent: that is, to the north. Since the Tropic of Cancer runs well to the south of the Greek world, no one Herodotus could count on as a trustworthy witness had ever seen the noonday sun in the north, and so he dismissed the tale of the Phoenician voyage. But we know the Phoenians were probably telling the truth, and that they accurately reported something very surprising.
This is a nice illustration of Bayes' principle, which says "surprising information should make the biggest difference to what we believe." This is a difficult principle to apply because surprising information is also the most likely to be wrong, which means the practical rule is “well-verified surprising information should make the biggest difference to what we believe." Our response to surprising information—which is potentially extremely valuable—should not be to dismiss it, but to test it for veracity.
Herodotus, to his credit, reported the information even though he didn't think it was reliable, in keeping with his technique of reporting what people believed even though he thought it was nuts. He did believe tales of lions the size of ants being used to mine gold in the Caucuses, so we should be grateful he didn’t restrict himself to what he found plausible.
Despite minor contacts of this kind, major trade--mostly between Arabs and Africans, and mostly in gold, salt, and slaves--was only developed in the post-Roman world, and grew to real significance during the Middle Ages.
This means there were a number of unique technologies that developed in sub-Saharan Africa and were never exported beyond it, such as this method of refining gold by melting it in glass.
Even after smelting gold is often mixed with other minerals, particularly metals, and further refinement is desirable. Arab and European goldsmiths developed a variety of techniques to do this, but the Malian method described here was unique: partially refined gold was melted with glass. Gold and glass are immiscible, which means they separate like oil and water, while most of the common impurities dissolve in the liquid glass and then get "frozen in" when the mixture cools. This allows the purer gold to be recovered from the slug.
Furthermore, the process appears to have used primarily recycled glass from broken bottles and the like, so it was both effective and efficient.
It's unclear how much more "hidden history" there is in sub-Saharan Africa, but everything we know suggests "a lot" is the most likely answer. The Golden Rhinoceros is a recent book that describes what we know of the African Middle Ages, mostly through the eyes of Arab merchants, who pioneered trade routes through the Sahara and into the Sahel, the wide band of semi-desert that forms the southern "shoreline" of the Saharan sea. The book is a series of snapshots of different times and places where we happen to have enough information to reconstruct a little of the past, from fragmentary accounts by Arab travellers to the archeological remains of an abandoned caravan, which tells its own tale of life and death in the desert.
Throughout the Middle Ages the kingdoms of the Sahel traded across the desert with the Islamic kingdoms to the north, and they acted as buffer states between the tropical kingdoms of Central Africa, taking the always-lucrative position of middle-person between the kingdoms of Central Africa and the Islamic Mediterranean states.
Gold was the major trade good through the Sahara to the north, as shown on this interactive map of the "Gold Road".
Trade relationships tend to be the dominant form of international intercourse when there is the possibility of circularity or exchange: when both sides have to have something the other wants. In the absence of this, there is a tendency toward imperialism and conquest. In the Medieval Sahel, trade dominated because there were opportunities for mutually beneficial exchange.
Central Africa is deficient in sources of salt, which made its importation from the north in exchange for gold, ivory, and slaves a practical alternative to imperialism, which is always more expensive than trade because armies, like police, cost money. Salt was so much in demand in Central Africa that it was at times worth very nearly its weight in gold... but you had to get it across the Sahara first.
That was done by camel caravan, which was one of the great organizational innovations of the Arab world. Camels had been used to cross the Sahara since at least 3rd century BCE, but Arab traders introduced the use of camel caravans on a large scale, allowing a level of trade that was hitherto unprecedented.
While I'm not precisely a technological determinist, it is often the case that technological possibilities and limitations play a considerable role in history, and just as the camel opened up the Sahara for trade, the susceptibility of camels to tropical diseases made them useless beyond the Sahel. This, as well as the unsuitability of mounted camel military tactics in the jungles of Central Africa, helped limit imperial ambitions.
The Sahel is also the site of the Bodélé Depression, a 500 km long, 160 km wide, former lake-bed in southern Chad that is the source of regular dust storms that sweep across West Africa, carrying so much material (up to 700,000 tonnes per day!) that it's a significant source of nutrients for the Amazonian rain-forest on the far side of the Atlantic. The Earth’s atmosphere tends to be much more strongly connected running along lines of latitude than longitude: atmospherically, we live on a banded planet, where it’s the oceans that are primarily responsible for north-south circulation. Nowhere is this banding more apparent than Africa, which lacks the long mountainous backbone of the Americas to break up the pattern.
We still know very little of the various kingdoms of Medieval Central Africa that lay beyond the Sahel. The fact that they were non-literate and located in areas where jungle would consume a city a few generations after it collapsed--which cities have a tendency to do--makes the process of rediscovering them arduous, but there are bound to be wonders of human ingenuity yet waiting to be uncovered.