With almost all of the site licenses, we looked at previous year's data and negotiated agreements that would cost no more that what we were spending. There is no charge for this service. It actually runs the installation program on the local workstation. So you don't need 20 free megs to install a 10 meg application. This covered all the costs for manufacturing including creating a master, file to film conversions, printed disk sleeves, shrink-wrap, and shipping.
Later orders cost less since they already had a master and film on hand.
The price per CD is adjusted for volume. We've looked into electronic charge-back but can't get past the headache of administrative overhead. For most of the licenses that we can obtain in volume, the cost is so low that we can't justify doing it ourselves. If it's not a true site license, we generally let the vendor handle distribution. Our Departmental Support Lab will provide backup services to the vendors if there's some urgency or an immediate need.