I'm quite sure i've seen this request or even an add-on before that did this but can't quite find it.
I think what would work really well for some stores is the following setup:
1. Customers goes to checkout/view cart and gets regular/default shipping method by default.
2. Customer can check a box for tracking (adding ie 3 Euro costs) or a box for priority shipping (adding an x amount depending on location).
What do you guys think?