Ontology of Folksonomy: A Mash-up of Apples and Oranges is a great article explaining the individual benefits of both ontologies and folksonomies, and how they can potentially integrate together to aid data interoperability.

An excerpt:

The attack on “ontology” is really an attack on top down categorization as a way of finding and organizing information, and the praise for folksonomy is really the observation that we now have an entirely new source of data for finding and organizing information: user feedback. For the task of finding information, taxonomies are too rigid and purely text-based search is too weak. Tags introduce distributed human intelligence into the system. As others have pointed out, Google’s revolution in search quality began when it incorporated a measure of “popular” acclaim — the hyperlink — as evidence that a page ought to be associated with a query. When the early webmasters were manually creating directories of interesting sites relevant to their interests, they were implicitly “voting with their links.” Today, as the adopters of tagging systems enthusiastically label their bookmarks and photos, they are implicitly voting with their tags. This is, indeed, “radical” in the political sense, and clearly a source of power to exploit.