My wiki, http://vidwik.org, is about cataloging music videos so my goal was to create a some what Media Player like UI experience.
The first place I used categories was to alter the side navigation bar I show when a user is on an artist page versus a help page.
The second place I use categories is to generally partion content and give myself the ability to later lock down who can edit certain type of content. All of my music genre and artist index pages go into "genre:" & "artist:" categories because I may latter want to say any members can add new artists but only administrators can modify the list of genres.
Another reason to categorize is because a lot of the various wikidot modules let you pass in a category to filter by. For instance, if you look at my main page you'll see lists of Top Rated and Recently Added artists. I can filter to only artists because all artists pages are in the _default category and I don't keep any other kind of content in that category. I chose to use the _default category for artists because I wanted pretty URLs for bands.
In fact, you may notice that "Home" is listed as the top Recently Added artist. That's because I still have my root welcome page in the _default category and there seems to be a bug that anytime you add another page it bumps "home" to the top of the Recently Added list. I need to move my "home" page to another category to fix the issue and ensure that only artists show up in the list.
-steve