Juju \JOO-joo\ , noun;
1. An object superstitiously believed to embody magical powers
2. The power associated with a juju
The Oxford English Dictionary actually has three different entries for juju or ju-ju. The first is similar to the given definition: "An object of any kind superstitiously venerated by West African native peoples, and used as a charm, amulet, or means of protections; a fetish. Also, the supernatural or magical power attributed to such objects, or the system of observances connected therewith; also, a ban on interdiction effected by means of such an object (corresponding to the Polynesian taboo)." The etymology for this definition is uncertain, but it's definitely West African and possibly from French joujou, meaning "plaything."
Another definition is: "A style of music originating among the Yoruba people of Nigeria, characterized by lyrics drawn from the traditional praise songs, proverbs, etc., and typically an instrumental backing of intricate, melodic guitar lines and complex polyrhythms played on a range of percussion, [especially] talking drums." This etymology is also uncertain, but it's possibly from Hausa jùujúu, meaning "fetish"
The third definition is: "A marijuana cigarette", which is a reduplication form of (mari)ju(ana).
I have a feeling that the reason these etymologies are 'uncertain' is because they are as old as time. This idea of superstition and protective charms is as old as the human race and a word like juju could have been made up a thousand times by a thousand different people to mean something like this. Obviously there's nothing superstitious about the sounds involved - sounds are sounds, they don't intrinsically mean anything - but a simple, reduplicated word could have come from anywhere at anytime. I also have a suspicion that the marijuana juju has much more to do with the magical juju than the actual word 'marijuana'. I don't have any real evidence, but if juju has been in the vernacular meaning something magical it could be easily applied to marijuana - plus no one really pronounces the -ju-.
*Today's word and the first definition were both taken from Dictionary.com's 'Word of the Day' for Monday, October 25