Having just had a horror United Airlines recently, I found this report very fascinating. US News used information produced by the UN Department of Transport and produced an excellent slide show.  Best to worst

1. Hawaiian Airlines (excellent on time performance and customer satisfaction ratings)
2. AirTran (high customer satisfaction and good baggage handling)
3. JetBlue (great customer satisfaction)
4. Southwest ( lowest % of customer complaints)
5. Continental  (consistently good for six years)
6. Frontier (similar rating as Continental)
7. US Airways (scores have been improving)
8. American (the worst airine for baggage losses)
9. Alaska (good on-time performance but passenger dissatisfaction)
10. United (with the lowest passenger satisfaction score)
11. Delta (most delays and most passenger complaints)

From my own experience, this is my current rating of the airlines in the USA (notice some overlaps!)

1. Virgin America-everything about VA is class-hope they can hang onto this as they expand
2. JetBlue
3. AirTran- 
4. Southwest Airlines-
5. Frontier Airlines
6. Continental
7. Alaska Airlines
8. United Airlines- 
9. American Airlines 
10. US Airways 
11. Delta