One way that has been suggested for this in the Core Plot framework was to create two scatter plots within a single graph, have the higher one use a colored fill, then have the lower one use a fill of the same color as the background of the graph. If you order the plots so that the lower one renders after the higher one, it will effectively mask off the lower portion where they intersect and leave only the area between them colored. The Baby Bump iPhone application does this with their Core Plot graph (see the third screenshot on their product page).
It would be more elegant for us to support this natively, so we might want to add this capability to the framework.