I guess you need to do a lot of research before actually buying the DSLR.
Autofocus is VERY, VERY important. You'd have to focus manually for lenses that don't have internal autofocusing motors. The D5000 lacks the AF motor and thus it limits the amount of lenses you can use, since you'd have to get lenses with internal AF motors = More money.
Read the forums and FAQ of the website I provided, you'll learn many things you didn't know and maybe you'll understand why I say the D90 is better than the D5000