Advantages: Focus motor built into the body allowing Auto Focus with many lenses that don't have a silent wave motor built in. The D3000, D3100 and D5000 don't have that. The D90 also has one of the best "high ISO to low noise" ratios in the Nikon fleet. Some reports say that only the D3 can beet it for low noise. It has many of the same features of the high end cameras and will produce pictures equal to a D300. It is a truly versatile and competent camera. I love mine and most everyone that has one loves it.
Disadvantages: It is not weather sealed. Has 11 focus points (not a disadvantage but the higher end Nikons have 52), Higher price than the D5000. Can you really call these disadvantages? That is up to you.
Mark