Clay Shirky thinks that ontology is overrated. See Ontology is Overrated: Categories, Links, and Tags. This is an interesting (and popular) take on classification. Though he is mainly interested in the Internet, his view also appears to have implications for personal note-taking.
His related post on The Semantic Web, Syllogism, and Worldview is also relevant in this context.
See also my earlier entry on Weinberger on Pepper on Topic Maps.