A local landscaper would be able to actually take a look at your drive and its surrounding area and possibly make some suggestions, but I can tell you at least a little since I also have a gravel drive that used to occasionally pool.
Over time, gravel drives tend to get low in the center. They need to be at least flat, if not crowned. Then, they either need to be higher than the surrounding grass or whatever (if they do not readily drain down quickly), or else they need some kind of drainage system underneath them. To drain away water from right next to my house and in front of the garage, I have a deep, rock-filled trench running from under the drive in that area and on over into an area away from the house that drains much better. However, your own solution might be as simple as having another load of gravel dumped and spread in the area that tends to flood.