Drupal is great and the taxonomy system is great - but large taxonomies (over 1,000 terms are a headache for any system) and Drupal is no different. I have a new taxonomy for a project with > 5k terms in a three deep hierarchy and using it presents some usability, performance and other issues.
So I though I would take a break and write a bit about evaluating some Drupal contributed modules for working with large taxonomies: