Ten Fastest Marathons by an American (As of 10-27-06)
2:05:38 Khalid Khannouchi London 2002 (#3 All-time)
*2:05:32 Khalid Khannouchi Chicago 1999 (#4 All-time)
2:05:56 Khalid Khannouchi Chicago 2002 (#7 All-time)
2:07:01 Khalid Khannouchi Chicago 2000 (#54 All-time)
2:07:04 Khalid Khannouchi London 2006 (#59 All-time)
2:08:44 Khalid Khannouchi Chicago 2004 (#319 All-time)
2:08:51 Alberto Salazar Boston 1982 (#364 All-time)
2:08:53 Dick Beardsley Boston 1982
2:08:56 Abdi Abdirahman Chicago 2006
2:09:00 Greg Meyer Boston 1983
2:09:21 Alberto Salazar Fukuoka 1983
So Khannouchi has the 6 fastest times by an American, and still has the 5 fastest if you throw out Chicago in 1999. His best is 3 minutes faster than the second fastest American. He has 6 times in the top 350 All-time, and no other American has any. He is the only American to hold the world record in the marathon since 1963. His only blemish is his lack of olympic medals.
I think you would have to say Khannouchi is better than Rogers and Salazar becasue Khannouchi's times are faster and Rogers and Salazar have no medals either. Meb has a silver in Athens, but has only run 2:09:53, almost 4 minutes behind Khannouchi, good for only the 12th fastest American and the 21st fastest time by an American.
That leaves us with Frank Shorter. Shorter never held the world record, and his fastest is only 2:10:30, not even in the top 1000 All-time. Kannouchi's would have finished nearly 5 minutes, or almost a full mile in front of Shorter. However, Shorter has an Olypic gold in Munich and a silver behind a confirmed doper in Montreal. There are 5 or 6 races a year where the World Record could possibly be broken if the conditions are good (Chicago, London, Rotterdam), but the chance to win an olypic medal comes on a single day every 4 years.
So I believe the question of is Khalid Khannouchi the best American marathoner of all-time boils down to this: Khannouchi vs. Shorter, what defines greatness, World records and total domination of the all-time list, or Olympic medal count?