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:

• Taxonomy Super select: Changes the multiselect box to check boxes - chokes on large lists
• Taxonomy Tree Select: Promising and uses JQuery to create a tree view from a hierarchical taxonomy - but chokes on large taxonomies
• Hierarchical Select: Promising and works well - but also fails with large taxonomies.
• Big Taxonomy Autoselect: Perfect if you know the term you want to add as it autocompletes (showing the hierarchy path and the term id)
• Left and right: Contibuted a patch and will report back on how this works out - looks like it will be the solution.

Generally any user of large taxonomies (1k+ terms) faces the same issues: database access and large returned result sets, client side processing and timeouts on requests and database connections - or simply horrible user experience of large large lists. We developed a solution for the NHM ten years ago which provided an efficient query path using warehoused relations allwoing the speedy navigation of taxonomic hierarchies - I think we need to port this to a Drupal module - see it in action here.

I'll update this post with more 'large taxonomy' conclusions and issues once I have completed this phase...