For the rest of this year I'm using Drupal's book module for a substantial collaborative research document (250,000 words, 50 authors, 130 peer reviewers). This is a useful project to test Drupal's ability as an academic authoring tool, and I will document some experiences as I go along, hopefully working towards a longer howto article for later publication (and perhaps a collaborative authoring branch of drupal-on-a-stick).
general comments
--> for those working in a windows environment, particularly when working with technophobe colleagues, the drupal-on-a-stick project is fantastic (http://www.ratatosk.net/software/onastick) and encourages people to try out drupal at home
--> for new users, it's worth buying one of the Drupal books as a desktop reference.
--> the process of choosing, installing and relevant modules takes time. While it makes sense to keep Drupal core simple and to encourage the plug-in process, Drupal.org should perhaps begin a series of 'use cases' or 'kickstart lists' to get users up-and-running quicker (e.g. 'drupal for academic authoring', 'drupal for media content', 'drupal for media screening', 'drupal for magazines')
drupal for academic authoring - kickstart list
For academic authoring, the list of relevant (non-core) modules is as follows: