In the end, there's no "wrong" decision. You will have fun and take good pictures no matter which camera you end up buying. So view the following as just suggestions - I promise you'll be happy no matter what you end up buying.
If you're the sort of person that will probably buy this camera and then use it for as long as it lasts, get the D60. The D60 is newer, which means the sensor technology is newer. The main advantage to this will be somewhat better low-light, high-ISO shooting compared to an older sensor that has the same resolution. Not amazingly better; just incrementally better.
If you're the sort of person that will likely buy a newer, better body a couple years down the road - get the D40. It's not going to matter for the photographs you take now. With the money you save, you can buy another lens (or a better kit lens).