A swift perusal of some interesting things you can do with taxonomies: flagging content for particular purposes, bookmarking systems, syncing post types and taxonomies, and syncing terms between sites in a multisite.
As always, the slides are only part of it, but do give you a flavour.
Plugins mentioned (if they're our plugins, and they're on Github, consider them move relevant to developers):
https://github.com/cftp/feature-posts-on-root-blog
https://github.com/cftp/sync-post-types-to-taxonomies
https://github.com/cftp/universal-taxonomy (mentioned in the questions)
Blogposts mentioned:
http://alexking.org/blog/2011/08/29/wordpress-post-meta-taxonomies
http://webdevstudios.com/2013/07/08/replace-wordpress-default-taxonomy-metabox-with-a-radio-select-metabox/
Tickets mentioned:
http://core.trac.wordpress.org/ticket/14084
http://core.trac.wordpress.org/ticket/15475
http://core.trac.wordpress.org/ticket/10142
http://core.trac.wordpress.org/ticket/17646
http://core.trac.wordpress.org/ticket/14084