Great info, but the only thing I would suggest opposing snipe is to learn how to use the 3 manual modes first.
If you learn how to use each manual mode (Fully Manual, Aperture Priority, Shutter Speed Priority), and using the different ISOs, you'll learn much faster, and understand photography much better. You won't have that "cushion" that tells you "this is too complicated for now, I'll shoot on an auto mode."
It will be very frustrating at first, but once you get good shots by doing the adjustments yourself, you'll feel so gratified.
The d90 is an awesome camera to start with; I just purchased the "newer" model, the D7000. It has the advantage of having a slightly better high-ISO performance, but the D90 is still very capable of doing so.
My first suggestion would be to buy a 35mm or 50mm F/1.8 lens, which will give you a great understanding of DOF, and how aperture works. It's also great for low-light, without needing a flash.
For now, I suggest setting your ISO to 800, and shooting in Aperture Priority (Av mode) unless you're outside. If you see that your pictures are blurry, it's probably cause there's not enough light coming in. Either zoom-out (i'm guessing you have the 18-55, or 18-105), or make sure your Aperture (f/ number) is at the lowest number possible (probably f/ 3.5)