"An upper ontology attempts to create an ontology which describes very general concepts that are the same across all domains". As almost always there is a Wikipedia article about this. Given that the subject is difficult, there is since August 2006 a request to clean up this page .. I have to agree that the subject is interesting and potentially controversial.
For OmegaWiki, an upper ontology is one of those things.. An upper ontology defines the broad strokes, and while it descends downwards more and more aspects may be inherited from higher levels. This means that an upper ontology has practical implications. It also means that we will eventually have in effect an upper ontology by default.
As an upper ontology creates the concepts that are true across domains, Wikis for Professionals will want to define how their ontologies fit into the upper ontology. As they are bound to have overlaps with other domains, there will regularly be found to be in conflicts between domains. As one WfP needs to link into other domains, the question of primacy will raise its ugly head. One WfP was there first, but this other domain is not its competency... A new WfP does have the competency but is disrupts the existing WfP...
An initial selection of an upper ontology will be crucial, its evolution will be exceedingly important when OmegaWiki will is to be bound by the integration into it. Personally I expect that a different model will arise; one where on the one hand great care will be given to the evolution of the upper ontology while on the other hand functionality will be created irrespective of the upper ontology.
Consider, when you know that something is a plant, you can infer all kinds of things about it. It is not really necessary to know how it fits in the greater scheme of things. It would be nice, but it is not required. When a lot of functionality is determined in such a way, there will be the question how this will fit together; it is therefore my prediction that these two forces will eventually find a balance. As OmegaWiki matures, this balance will become increasingly stable.