The Harry Potter ride, or FJ (for Forbidden Journey) as it's known here, has a very detailed queue that you go through while you wait to ride the actual ride. The queue is an attraction in and of itself, as it includes many recreations of areas within Hogwarts Castle. Because of this, many people (myself included) enjoy lingering in these areas to enjoy the details and take pictures. Some of the points of interest in this queue include: Dumbledore's Office, the Defense Against the Dark Arts classroom, the Gryffindor Common Room, the Portrait Gallery, and the Greenhouse. Several of these rooms have lifelike recreations of the characters talking to you or each other.
The Castle Tour queue is a way for those only interested in seeing only the queue to wander through at their own pace. It is a separate queue that, in many places, parallels the main queue, but without the option to ride FJ at the end. However, be aware that the CT queue does not include the Greenhouse nor several other minor areas not mentioned above, and also routes you through a different Portrait Gallery.
The point to remember is that the main queue has all the elements, but since it feeds people onto the ride itself, can move slowly at points. Conversely, it can also move quickly at other points, causing those going through to miss some of the details. The CT queue does not have this issue as it is specifically designed to accomodate those who either do not wish to ride, or would like to take their time in seeing the elements in the main queue.
Hope that answers the question!
