Over at the Plone Blog is the article Death and Taxonomies; it reviews Drupal's taxonomy (aka category) system.

The author basically comes to the conclusion I have, a conclusion that is shared by many in the Drupal community but not so much outside of it: Drupal's taxonomy system is amazing.

For most people and their uses, it is completely overengineered and complicated to use. This fits into Drupal's marketing stance that it is a content management framework rather than just a CMS. It is very generic, and with some custom programming can be adapted to anything--the possibilities are limitless. With many web development projects (that I don't want to write in PHP) I think about, I wish I had the facility of Drupal's taxonomy system.

Of course, there are problems, which the review goes into: there are too many hierarchal relationships in Drupal, all competing with each other. There is the menu system, the book module, and hierarchal taxonomies. The key to being a Drupal master is know when to use which and how to use them, something I've definitely not mastered. And that is part of the problem--why should you need to?