To the best of my recollection, Lionel's Ambassador Program ran from from 1998 through 2000. Train enthusiasts could apply to become an Ambassador. Upon acceptance, you were given points for assisting Lionel in a variety of events. Some of theses included assisting at a Lionel event sponsored by a local Lionel dealer, helping Lionel set up for an event and so on. If you accumulated enough points you could earn a bronze, silver or gold level special Lionel car. Of these cars, the gold level ones were the most rare as few ambassadors earned enough points to qualify. In addition to the cars there were also awards of specially labeled Lionel Jackets. During the three year duration of the program, Lionel held two Ambassador conventions - the first in Durango, Colorado and the second at the Carnegie Science center. Awards were presented at these conventions. 

Choosing a particular car to label as the most rare of all is a difficult and subjective task. The most desirable items change over time and basically comes down to a question of just how important a particular piece is to you.