I have done a lot of research over the past 6 months and finally purchased a 2006 QX56 in January. We purchased the QX for my wife and 3 small kids while I will now drive the Lexus LX that previously was the wife's. I have to say, that is looks like any of the issues with the car in 04/05 have been fixed now. The truck is quiet (will never be as silent as a car), solidly built and has the BEST features. I was ready to buy a new LX, but opted for the styling of the QX and frankly a lot more room too! I hate that the Lexus seats fold up against the windows in my LX - but this is no problem in the QX. This car feels like it will last a long time. The comfort is unsurpassed.
Nav system is great. Compared to my Lexus, the system speaks actual street names, not just "turns" - you barely need the manual if you are a little computer savy. I love the rollforward rear seats, the one-piece tail that also has a working window if you choose, and of course the incredible engine
Really nothing. I wish the gas mileage was higher, but for a 6,000 lb truck with V8, it really is not bad.