Hunter division is akin to the pleasure division in the Western horse industry. The emphasis of the judging is (or should) be on the horse -- his conformation, manners, way of going, and jumping style. The jumper division is the gaming of the English world. What counts is the time and leaving the course intact. No style points, but having solid control is a big help. That is the basic difference, but specific lists of faults can be found in the rulebooks of most associations, club shows, etc.
Scoutrider's right. Hunters also get points off for getting the wrong number of strides between fences, cutting corners, etc. Jumpers can cut all the corners in the world and get any # of strides, as long as they don't knock any poles down.