I was a fan of WP-SNAP!, which did make glossaries very easy to manage. However, WP-SNAP! was not aware of the new taxonomies and was category-based on "normal" articles, did not have hovertips, and didn't use shortcodes. Worse than that, the WP-SNAP! author gave up on the plugin.
WP-Glossary does everything that WP-SNAP! does, but it does everything better. Glossary entries are taxonomies, so they won't populate the loop with garbage (which was a handicap with WP-SNAP!) — unless, of course, you wish them there. The shortcodes are easy to do and understand (although I would rather prefer the ability to search for related content, which is what you get when adding a new link to another article, instead of "guessing" what the right entry is named). Adding an indexed page (with entries for A, B, C etc.) and styling it just needs one shortcode; all the rest happens automatically.
I did test some alternative free Glossary plugins (there are many which are paid). While all of them sort of work in a similar way, WP-Glossary, for me, was the easiest to setup and the easiest to use — many others have issues with URLs and rewriting rules, which WP-Glossary has not. This is particularly important for me, since I use Nginx, and although many WP plugins are Nginx-aware, a lot rely upon Apache's mod_rewrite module to work properly. WP-Glossary works right out of the box under either Apache or Nginx.
Also, it continues to be kept up-to-date by its friendly author, which means that not only security issues are handled quickly, but that new features might be developed (like the recent move to a completely new "hovering tip" engine, qTip).
While few plugins are "perfect" and "complete", I nevertheless can fully recommend WP-Glossary as an excellent plugin which does pretty much what is needed and is simple to install and use.