At the end of 2013, Apple delivered on it's promise to provide a simple way for MDM (mobile device management solutions) such as Apple Profile Manager, Casper or AirWatch to install and revoke apps to iOS devices over WiFi and the Internet.
It's call "Managed Distribution" and makes it easy to deploy (and revoke) apps for 1:1 iPad programs in schools, where each user has a device for themselves. Whether it's school provided or a BYO program, it makes distribution of institution owned apps straightforward.
If you are using Apple Configurator, you can still purchase apps in the VPP Store and download the 'Redeemable Codes' spreadsheets. This method is still the best for most schools who have shared iPads in class sets or small groups shared across the school.
BEWARE – When buying apps, choose the right option:
'Redeemable Codes' for Apple Configurator
'Managed Distribution' for MDM