I'm still working on this. I've got a test index running on a shared hosting server, and the performance seems to be noticeably different than on my local machine that had nothing better to do, but some other factors changed as well, so that may not be a totally fair assessment.
I've got two versions, in one, I'm storing the categories in a text field, and in the other a varchar(255) - obviously some get chopped off in the varchar field. There are noticeable difference in some queries but not others. I'm hypothesizing that this is due to smaller datasets, but my tests so far aren't confirming it. I also seem to be experiencing a lot of noise in my result times from it being on a shared hosting server.
Anyway, the scripts are at http://aerik.com/wikintersections.php (text field) and http://aerik.com/wikintersections2.php (varchar field, truncated category list)
It takes the text in the input box and drops it in a boolean fulltext search of the categories.
I know it's an ugly/nonexistent UI and so forth, but I wanted to invite any interested parties to test and brainstorm with me.
Thanks, Aerik