Very nice looking site. I wish I could comment inline, ala hgbook.
Regarding tags: full-text search will be much more useful. I’m not sure how you might pull that off though, other than providing hooks for lucene.
Hierarchy, on the other hand, is completely necessary, both for organizing large knowledge bases, and for very large teams that require privacy in certain cases. This is assuming that you’re willing to allow Access Control Lists in Pylowiki. Mediawiki objects to this in prinicple.