I did find one interesting note on the Airline Quality Rating report released by researchers at Wichita State University and the University of Nebraska at Omaha. AA did beat out American Eagle.

From best to worst, the airlines ranked as follows: JetBlue, Alaska, Southwest, America West, US Airways, Northwest, Continental, AirTran, United, ATA, American, Delta, American Eagle and Atlantic Southeast (Source: The FrequentFlier Crier ISSN 1538-862X Issue #291 -- Apr. 7, 2004).