I'll add to what's been said, AF-S will be quieter and (in most cases) faster AF, and it has been pretty much proven AF-S allows more consistent accuracy in focusing. This isn't surprising given that the AF motor can be sized appropriately for the lens, and have less mechanical linkage. It's a much more tightly controlled system.
Therefore, AF-S is the generally desirable AF system.
At the time the D40 was introduced, I considered the lack of AF motor to be a serious deficiency. Now, most of the holes in the lineup have been plugged so that it's not so much an issue any more. Indeed, unless you intend to autofocus with legacy lenses, it's something you'll never miss.
I lost a lot of old lenses in a burglary, and my new kit contains only 1 screwdrive lens (AF 50mm f/1.8D). If were compelled instead to replace this with AF-S 50mm f/1.8G, for body compatibility, I wouldn't have considered it any big deal.