I often need to link to custom taxonomy term archive pages and would love to be able to do so through the AJAX internal link navigator added to the visual editor in 3.1. Is there any way to get this functionality, with either with a plugin or non-colossal changes to the core?
Right now there are no hooks to do that from a plugin and the function that makes the search query itself is not pluggable which means that the only way to achieve that is to hack core files.
Currently there is an open Trac Ticket asking for some kind of hook.
Here is the WordPress Trac Ticket associated with this functionality. And here is how to get the list of taxonomies. The code for the internal linking is in /wp-admin/includes/internal-linking.php. This is the code you would have to modify via a plugin (I’m not quite sure what hook you can use).