I personally think that the Skytrax survey vastly underrates the Japanese airlines, and I would be curious to hear what all of you think.
I don't have enough experience with all the alleged "five star" airlines to comment directly, but I've noticed over the years that the FT forums on airlines like SQ, CX, and EK have FAR more complaints than the NH and JL forums. And when you read the individual negative experiences of these airlines, often they are things that would be unimaginable on NH or JL (rude staff, incompetent rez agents, terrible handling of irrops).
Comparing all the trip reports I've read over the years on the Japanese airlines vs. the "five star" airlines (and considering the flawless experiences I've had over many flights on JL over the years), I really don't understand how airlines like EK and CX get their five star ratings and why the Japanese airlines aren't rated higher.