I have similar situation. Some items in our cart will not have any shipping involved and even though I entered 0 for weight it still gets a quote from UPS ,
What do you mean drop in a check to skip an item here , could you elaborate?
"You could store the free shipping identifier in a new column in the cart, then within the loop for the shipping quote you could add in a check to skip that item if the column has a particular value"
the loop you mean in the page where the item has the add to cart button? or in the shipping rules for the cart?
**We need to solve this today. A separate cart for items without shipping configuration would be a 'fast' solution but not practical for a customer to have to go thru 2 different and separate checkouts.