Prospecting is something jewelcrafters can do to turn ore into raw gems. It takes 8 seconds of pure casting time to prospect a stack of ore, as well as whatever time it takes you to look all the gems out of the four loot windows that entails. It can't be legally automated, so that makes prospecting the semi-porous membrane between the ore and raw gem markets. Without this barrier, the relationship between the prices of ore and raw gems would be more like the ore and bars in which unless you have a small market with no active miner auctioneers, the price of bars isn't usually much more than the ore that went into making it.
As it is, you may often find the price of ore is much lower than the gems you get from prospecting it are worth, even if you just sell them raw on the auction house. The reason for this is that mining ore is hard enough, and many times, miners will just throw their wares into the AH and rely on the market to snap up any ore below the price where prospecting is profitable. Also, unless these miners happen to be (or have) jewelcrafters, they may not exactly know what their ore represents in terms of raw gem money. Enter Wow Prospector, which allows you to input the price per ore and for the raw gems, then output whether it's worth prospecting.