Thom Hogan mentioned, in no uncertain terms, why he prefers the Nikon D90:
If you’re looking for the best tool for producing the best possible photograph, there’s little question in my mind that the winner there is the D90. Indeed, I’m not sure how you can say otherwise. The D80 is actually my LEAST favorite of any camera Nikon has produced since the D70. It hot pixels worse than any other Nikon, Nikon never fully fixed the amp noise issue, it has the least capable high ISO JPEG from the same sensor as other Nikons (the D60, for example), and the matrix metering is horribly off-kilter. THAT’S a “pure photographic tool”? Sorry, but it looks as if the D90 fixes all of those things, so it wins on that alone in my book.
In summary, the D90 fixes many of the shortcomings on the Nikon D80.
Read more in the Nikon D90 vs Nikon D80 article.