Over the last couple of years the UNT community has been steadily migrating to Drupal; we recently selected Drupal as the official campus CMS, and are currently running several hundred Drupal sites in production.

The university Central Web Support office (where I work) is tasked with managing the Drupal instances we give to folks around campus, along with applying security updates, end-user documentation, and other general support services. We face a number of unique challenges in this capacity:

1. How do we maintain a consistent look and feel throughout the enterprise?
2. How do we ensure a reasonably simple user experience, especially when many of our users are non-technical folks saddled with web responsibilities on top of their usual jobs?

Appalachian State University has put together a very informative set of resources for its clients; of general interest is the "Benefits" page, which could be of use to anyone trying to convince a potential site admin to use Drupal.

Dries Buytaert maintains a list of education sites using Drupal; definitely worth looking through, especially if you're in the process of selecting an official CMS for your school and need some good in-the-wild examples.

Not sure how comprehensive this is, but it looks to be a very helpful list of educational institutions currently using Drupal. Also, it's a wiki page, so if your institution isn't listed, you can add it!