You would need to add some kind of flag in the products table to identify these products ...
Then you can display on the products that they are store pickup only ...
This could be done by adding this information when the price is displayed via the function for displaying the price ...
Then, you have to decide do you want to allow the customer to checkout when they have a mixed order of Products that can be shipped and Products that are Store Pick Up only ...
You could customize the checkout to have this displayed to the customer as a reminder and you could customize the email that they get on the order to display this and the customers Order History so that it shows this as well ...
Or, you can make it that Store Pick Up Only products cannot be purchased at the same time as Products that can be shipped ...
Or, you can make it that when Store Pick Up Only products are in the cart that ONLY the Store Pick Up shipping module is available ...
This really depends on how you want this to work ...
Some customers would prefer to have shipped to them anything that can be shipped and pickup from the store only what they have to ...
Once you make these decisions then you can proceed to customize your shop for this feature ...