Come check out a new Drupal education application:
http://www.humanitiesprep.org
This is an early-stage portal for a small high school in New York City. So far I have "integrated" Squirrelmail by way of a login form inside user accounts, and created some flexinode and webform content that allows form-based communication about student issues. Students and teachers all get a squirrelmail account and email address identical to their Drupal username. I modified the user module to make the "personal contact form" point to the users school email address, and all administrative (new password requests, etc.) communications point to the users' personal email address. Up to this point, I have had users join on a sign up basis, whence they must enter personal information about their full name, advisor, etc. This has cut down on the administrative load.
Another handy trick was to create a "select" CC field for webform module, which enables it to be more useful in an administrative setting, where multiple parties need to be kept in the loop on student issues.
Another coup was to use taxonomies that enable private, role based access to content. For example, student-published content, by default, is not public. Staff-only content, such as staff forums, can be kept private from students....etc.
The theme is a fairly minor tweak of the "fancy" theme.