I used to own a Nikon D40 and just upgraded to a D5000. I would recommend either of them. If you have the extra cash, go for the newer model.
I was in your exact situation, I had the money for an upgraded body but didn't exactly know if I should spend all of it on the body and which body to get or who to go with. I do bird photography so for me it was easier because most bird photographers get canon because of the lens lineup. I went with a canon xsi for a few reasons:
-TLi wasn't out yet
-much better than XS for very little money
-at a certain level without a very high end setup it will be very difficult to detect the difference of megapixels
-much cheaper
-more important than ANYTHING else in image quality is 1) experience and 2) lens. I didn't have either but knew that body was much less important. Now that I have both I completely agree
One thing I didn't see, and maybe I missed it, but have you held both Nikons and Canons in your hand, used the menu system, etc? It does help to have friends with the same lens system (and that helped me make my decision), but if you don't like the feel of the camera in your hand, I would wager that you're less likely to use it.
4, 5 months ago I was in exactly the same boat as you!! I was moving up from an 10 year old Nikon F4 (still using it though ). My first thought was getting a new one too. I didn't bought a new one and went with a second-hand D80. It was in perfect condition with 2 years additional warranty and less than 10k on the shutter. I got it for an amazing deal. This meant I had some money left for a new lens!! (I already had a some nice glass from the F4) So I saved some money the month after that and picked up a Tokina 12 24.
Seriously I'm so glad I didn't went with the D90. I learned so much with the D80 for far less money and I'm still learning with that super wide angle I got. Also having a built in AF screwdriver was very convenient for me because good lenses with dedicated AFS are a little bit more expensive and I saved some money with that. In the future I would like to buy a nikon AF 80-200 f/2.8 2-ring and with a dedicated "screw-driver" I save almost $750 on the 70-200 AFS. (the 70-200 is superior but it's not worth an extra 750 for me)
Really, The D90 has superior technology but a cheaper camera with real good glass is just in my opinion better compared to a D90 with kit lens for roughly the same price. (actually I came out cheaper as a D90 kit because I got some great deals)
All in all, If you're on a budget, go secondhand!! It just takes some time before you encounter a nice deal, same goes for the glass. You will not regret it.