Everyone seemed to miss your question.
I purchased the d90 after doing a bunch of research and I've loved it for the last 6 months. That said, the 5000 has the same sensor in a smaller body. So it is really easy to take the money you save buying the 5000 and purchase the 35mm 1.8 DX lens ($200). The two together are going to be a great combo and, honestly, really improve you as a photographer, and thus your photographs. A really great fixed prime will get you to move your feet, simplify how you line up a shot, and get you thinking about framing.
The main benefit you are getting out of the d90 is an autofocus motor built into the body, a boost in frames per second (which isn't necessary for most work), and (for me) a more comfortable fit in my hand. I think the low light shooting might be a little improved on the 90, but buying a flash (400 or 600) would be more within reach after not spending the extra cash on the 90 (plus the 1.8 lens means you wouldn't need the flash all the time).
Plus you get the articulated lens. I really don't get why all cameras don't have this... Maybe it looks too much like a gimmick.
Ken rockwell does a really good comparison check it out:
http://www.kenrockwell.com/tech/recommended-cameras.htmHe is slanted toward the 5000 + 35mm f/18 combo with a 400 flash, but with good reason.
If you decide to purchase this combo click on one of the links to it through Ken's sight. It puts some change in his pockets, and trust me he deserves it with all of the great articles on his site.
Cheers,
Knox