I was making a similar decision back in January to get either a D3000 or a D5000. I went with the slightly more expensive D5000 and was ultimately very happy that I made the decision. After briefly looking at a D3000 owned by someone else, I could tell I would've been a bit dissappointed if I hadn't opted for the D5000. So, given the choice between a D5000 and D3000, I would definitely opt for the D5000 hands-down.
However, there's also a part of me that wishes I got the D90. It would've undoubtedly been the better camera... the built-in focusing motor alone is a very attractive quality that the D5000 doesn't possess. At the time, however, I was buying a D5000 on D3000 budget... I just couldn't have mustered the extra cash for the D90.
Overall, the D5000 is a great camera for its price... I don't really feel any desperate need to rush out and replace it with a D90. The image quality between the two is pretty much equal, the video on all them really isn't spectacular anyway, and the D5000 does offer an articulated display which is not found on either the D90 or the D3000. Articulated displays are held as gimmicks by some, but quite frankly, I've found it to be pretty useful in certain instances.
In my heart of hearts, I certainly would like to have a D90, but I'll be happy with the D5000 for quite a while in spite of that. I agree with Derrel that a used D90 would be a great choice... I may actually end up buying a used D90 myself and using it in tandem with the D5000.