Over here in the UK, the situation is that it's taking less and less sales for someone to to get to number 1 in the charts. Wouldn't it be more useful if we included music downloaded (legally) over the Internet?
If you're talking about tracking downloads from major pay download services like iTunes and Rhapsody, then I'm sure Billboard or someone else is working on it. Those sales will have an effect on chart positions eventually, later if not sooner.
But if you're talking about free downloads from independent artists like Request-A-Song, then there's little hope of that happening. It would be tough to globally track and truthfully audit download counts from such a disparate group. Remember, products and services usually follow the flow of money, and where money doesn't go, the services don't go either. Even if we had a free downloads chart, I bet Billboard and the like wouldn't care about it because (a) the downloads aren't directly involved with making money, and (b) independent artists are outside the recording industry's realm of control.
As for independant pay-per-download artists running their own stores on the internet, the reasons a prominent chart doesn't exist for them is similar to the free-download reasons listed above. Rarely does enough money change hands to warrant any serious attention from music publications and businesses.
Benj
