A lot of what I do seems to include a dark subject with a well-lit background. My D90 has a strong tendency to focus on the background instead of my subject, even when the focus point is completely covered by the person. This is independent of lenses (it even does it with my manual focus lens if I'm trusting the focus indicator). I don't think it would be miscalibrated focus, since it does it with a variety of subject-to-background distances. It seems like the camera just grabs whatever it wants as opposed to just the focus point (I am in single-point mode, no dynamic area or auto selection).
I know I need to be finding contrast to help the focus system, but does anyone have some more extensive advice?