taxonomy_defaults 6.x-2.0

Compared to 6.x-1.0:
Overhauled interface
Better performance & scalability
Lots of bug fixes

Note: In order to upgrade your "hidden" vocabularies from 6.x-1.0 or earlier, you'll need to enable the vocabulary/content type relationship on the taxonomy administration pages, and then turn off the associated "Visible" checkbox. The resulting behavior should be the same, but with less likelihood of bugs and conflicts with other modules.