In the great academic tradition of paying people large amounts of money to devote years of their life pursuing knowledge whose contribution to the sum of human intelligence is questionable at best, the authorities in Uppsala University in Sweden commissioned a whole team of researchers a few years ago into answering this very question. They failed to come up with an origin except to agree that it is very old indeed and can be traced back to the earliest written records. However they did make a pretty good stab at affirming not only how ancient a habit it is but also why. Apparently it is to do with a principle called "social contagion" which manifests itself most clearly in making communal noise together to express a common view. It is easier to find examples of communal disapproval. However the same principle applies to approval and the communal challenge has always been how to noisily express approval that cannot be confused with the opposite, and using of course the tools available at all opportunities (voice and appendages).
All of this makes perfect sense until one then visits a Swedish auditorium and sees what exactly they're talking about. Like all Scandinavians (and some Northern European cultures) Swedish appreciation through applause is almost always performed in a synchronised fashion with everyone clapping at the same time. To other people's ears this sounds way too regimented and lacking spontaneity, in fact ominously like the derisive "slow hand clap" which through social contagion is used to communally express extreme disapproval in other cultures. Which of course raises the questions of how on earth this disparity arose, where did the slow hand clap originate, and crucially which came first?