As with other Wranglers, and the older CJs, Jeep Wrangler JKs now have the option of using either full or half doors.
JK full doors - Full doors will make your Wrangler more secure, will allow you to control temperature better, and will keep the elements out better. The down side is that they are heavier, and more difficult to take off.
JK half doors - There is nothing like coming out to your Jeep after work, and popping the upper doors off, stowing them in the back, and driving home with the wind in your hair! Half doors will allow you to secure your Jeep from the elements, then remove the upper half of the door at a minute's notice, replacing them if an unexpected shower creeps up. Wrangler half-doors are great, but they also have their down sides - fumbling with zippers can be a pain, and they don't insulate as well as full size hard doors.