As a system builder, I have alot of experience with motherboards and how their quality is over a large quantity of boards. Without a doubt, I have to say ASUS is the best. Asus has the highest quality over time. We rarely RMA ASUS motherboards. MSI has recently improved their standards, but we have experienced more problems with them in the past and they are not yet up to the low RMA rates of ASUS. Intel boards are of a similar quality level, but they lack the features that ASUS brings to the table.
Other manufacturers may put more features on their boards than ASUS, but for overall quality to features ratio there are none better than ASUS. MSI has made tremendous inroads and may eventually overtake ASUS, but not yet.