I'd advise you to check out exactly what the D60 has in relation to the D40. Believe me it's a lot: Like 10.2 mp--which for me is great since I print large images for my clients, and two methods of dust reduction--which, by the way, are awesome!!!!! I haven't had to clean this camera and I've had it a year--have to clean my D100 and D70 constantly after a few lens' changes; and the wonderful light weight--the reason some of the other cameras are more expensive is the material that they are made from--metal (more expensive and a pain to carry in the field) instead of the heavy-duty lighter-weight material that the D60 body is made of.. But in the long run, nobody knows how long one will hold up over the other. And by the time the lighter cameras' bodies give out newer, lighter, and more mp cameras will also have come and gone).
I'd list more reasons here, but you'll get more from your own research and not the opinions of people out there who do not own the d60 (or tested the quality of the images) or who really haven't researched it themselves and are saying what they have read or heard from other people who also haven't personally done this.
Now I'm doing what I'm advising you not to do, and that is to listen to a quote from another photographer close to me. He said that the D5000 is basically a "point and shoot" camera. I personally don't know how much truth is in this statement, but I do know, personally that one cannot say that about the D60.
Just some of my thought and opinions. To each his own.
Good luck on whichever camera you choose