Right now when you setup a configurable product, you choose attributes to assign to that configurable product which determine how to relate simple products to it.
I have a situation where there are a lot of simple products to assign to one configurable product, however some configurable attributes need to be optional. The optional configurable attributes would just come last in the sort ordering on the configurable product page. So if the next attribute is not assigned to that associated simple product, it wouldn't show -- only those configurable attributes of those with values would show.