Nikon every time for me! Find them far more erogonomically well designed and you don't have to use their software when downloading images.

I've got a D2x and D80, and my girlfriend has a D40.... all provide great results, generally the more you pay the nicer the camera is to use with less being hidden in menus (and more specialst features added as well).

Megapixels don't really matter a toss til you're printing over 16"x12"

VR is a great option, useful for panning shots and when you need to hand hold in low light.
If you can afford to I'd go with the D60 over the D40.... it'll just be slightly nicer to use.