I bought the D5000 and love it (my first dslr). From what I've read the D90 is the better model. The D5000 is supposedly better than the D60 with some of the D90 features.
They are both very capable bodies, I think you'd find that the D5000 is basically a replacement for the D60, whereas the D90 was a replacement for the D80. My biggest gripe with the D5000 would be its lack of AF motor as it really limits lens choices.