I didn't feel like reading through every post to see what each person had to add, but I think Unabomber hit it pretty spot on. I work in my local Nissan dealership's parts department.
I don't use the VIN to do each and every part that is ordered, but depending on what model and production date of car (down to the month), there can be many many choices, changes, and chances of getting someone the wrong part. If there is a doubt I ask for the VIN, which tells me exactly what is needed for the given car and prompts the program we use when searching parts to eliminate all the choices that don't apply. This is not used to screw you, but to help you and make sure that you are a satisfied customer.
When I'm doing a counter ticket (when someone walks in) and I ask for a VIN, it is only being used for the few minutes it takes me to find the part. It does not go on your counter ticket, it does not go into our invoicing database, it does not go into any super secret Subaru database either...it is not kept period. It is erased from the program the second I search for someone elses parts.
The service department does keep your VIN in order to track what services they have done to your car in case you have problems down the road.