Commerce Customizable Products
The only workable solution that I've come up with sits in a feature request in that module's issue queue; I haven't had a chance to try it out yet. Basically, I believe you can use a field on the product type as an options mask for the same field on the line item type. When a field is present on a line item type and shown on the Add to Cart form, its options will typically default to whatever is in the field settings. However, if you put that same field on the product type as a multi-value field, you could then use a form alter of the Add to Cart form to only show the options on the Add to Cart form that were selected for the product.

Again, this is just an idea - not implemented yet. But it seems like a very feasible way to accomplish what you want (and it's based on some architecture I actually helped a community member implement during a cocktail reception at DrupalCon Munich ; ).