We need to distinguish between Ontology as a Philosophical discipline and Ontological Engineering. You are asking about Ontological Engineering which is a new field that basically works out the fundamental concepts in a domain and the relations between them and the operations that can be performed on them. This is helpful in order to know what is or is not possible, or allowed, or present in a given domain. Ontological Engineering is useful because it gives the systems the ability to recognize the context they are operating in and reason about those contexts. Much of what ontology represents is what is called Tacit knowledge for us. It is representing this tacit knowledge of the world explicitly so that systems can negotiate their way in the world as we do. But at this time mostly very simple applications are being done in this regard. But there are some very big ontoogy building projects around like cyc (http://www.cyc.com/). Protege is the tool of choice in this market at this time and OWL is one of the major ontology development languages.
Ontological Engineering has a lot to learn from Ontology proper, i.e. philosophical ontology. An example is the problem of how to deal with Dynamic Ontologies. See Dynamic ontology evolution by Zablith, Fouad (http://oro.open.ac.uk/23527/1/10.1.1.141.3276%5B1%5D.pdf).
But Dynamic Ontologies is just the tip of the iceberg, there are five meta-levels of Being and current static ontologies that do not change as the context evolves is all at the Pure Being level. To incorporate dynamism they will have to transition to the Process Being level. And there are three levels of Being beyond that which they have not yet discovered. See my “Beyond Dynamic Ontologies to N-ontologies and the foundations of Emergence in Fundamental Ontology”. View charts are here: http://holonomic.net/MOBpalmerDO2004.ppt.