Good article.
A good example of the ontology problem is the Venn diagram. Unspoken in every Venn diagram is the white space that stretches as far as the eye can see. That's the world that isn't categorized yet. Anything could lurk out there.
The more Venn circles you draw, the harder it is to introduce new territories that intersect with all the territories they need to. Along comes the purple Malaysian wolfhound with an eyepatch and the scheme falls apart.
And that's with true/false categories. What authority can decide what's music and what isn't?
You think we'd learn from the Google example where they came in and blew away the guys trying to create a massive ontology of the web (Yahoo).
ref: http://www.shirky.com/writings/ontology_overrated.html