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.