Amaury Balmer

WordPress 3.1 and up allow for reasonably simple custom taxonomy, this plugin makes it even simpler, removing the need for you to write any code.
Add support for taxonomy with or without hierarchical. Choose the selector type for write post.
Allow to add taxonomy to any objects registered on your installation. This plugin can be coupled with the plugin ACF to a new term meta database that allow to create on fly any field need for the taxonomy. For example, for a “Number” taxonomy, you can add fields : number ID, date of parution, screenshot, etc !
This plugin is developped on WordPress 3.5, with the constant WP_DEBUG to TRUE.
This plugin allows you to add taxonomy just by giving them a name and somes options in the backend. It then creates the taxonomy for you, takes care of the URL rewrites, provides a widget you can use to display a “taxonomy cloud” or a list of all the stuff in there, and it allows you to show the taxonomy contents at the end of posts and excerpts as well. 
To boot, it comes with a set of template tags for those who don’t mind adapting their own theme.
For full info go the <a href="https://github.com/herewithme/simple-taxonomy" rel="nofollow ugc">Simple Taxonomy</a> page.

Simple Taxonomy

WordPress 3.1 and up allow for reasonably simple custom taxonomy, this plugin makes it even simpler, removing the need for you to write any code.

Robert O'Rourke

interconnectit

In addition to controlling your custom post type permalinks this plugin adds support for using custom taxonomies in your permalink structures as well.
Not only that but you can control the full permalink so the post type slug is not required at the start of the link.
Multiple post types can use the same permalink structure.
<h4>Usage</h4>
There are 2 ways to use this plugin:
Permalink Settings
The plugin adds fields to the permalinks settings page for any public facing custom post types.
In Code
When registering a post type you can add a value to the rewrite property with the key ‘permastruct’ to define your default permalink structure.
eg:
<pre><code><?php

register_post_type( 'my_type', array(
 ...
 'rewrite' => array(
 'permastruct' => '/%custom_taxonomy_name%/%author%/%postname%/'
 ),
 ...
) );

?>
</code></pre>

WP Permastructure

Adds the ability to configure permalinks for custom post types using rewrite tags like %post_id% and %author%.

Simple Taxonomy vs WP Permastructure