WordPress 3.0 is almost here, and the latest Beta 1 released last week is a good reference for what to expected. Some things were changed in the past 2 months with taxonomies in WP3, and here are new versions of GD Taxonomies Tools plugin to follow those changes.
WP3 now has a fourth default taxonomy for navigation menus, so plugin now recognizes that as a default. In the next week or so, new versions will be released again to improve on support for custom post types and adding taxonomies to them.