Get a used D50 for around $200, and enjoy a lot more new and second-hand lens access.
This is the only argument I can think for for NOT buying a D40. The D40 does lack the in-body focus motor. The only way to get the motor (and the ability to use motor-less lenses) is to either move up to the more expensive Nikon D80 or buy a discontinued D50 or D70 on the used market.
You have to decide if yu will ever want to use a non "AF-S" type lens. If you are happy being limited to AF-S then the D40 is a great buy.
Just do give this some thought. Either way is OK but to ignore the issue is not.
The D60 has 10MP as opposed to 6MP for the D40 (which also means more storage needed)
The D60 has a slower flash sync speed than the D40. Otherwise I believe these 2 cameras are identical.
The D40's fewer pixels give the D40 slightly better low light ability and the faster sync speed has the effect of making the flash slightly more effective for outdoor fill-in flash. But the D60's greater number of pixels will allow you to make prints that are slightly wider.
But in all the difference are minor. When you compare a 10MP camera to a 6MP camera the differences are proportional to the square root of the number of pixels. so compare 3162 to 2449, not 10 to 6. Differences are a factor of 1.3 not 1.6