In the context of knowledge sharing, I use the term ontology to mean a specification of a conceptualization. That is, an ontology is a description (like a formal specification of a program) of the concepts and relationships that can exist for an agent or a community of agents. This definition is consistent with the usage of ontology as set-of-concept-definitions, but more general. And it is certainly a different sense of the word than its use in philosophy.
What is important is what an ontology is for. My colleagues and I have been designing ontologies for the purpose of enabling knowledge sharing and reuse. In that context, an ontology is a specification used for making ontological commitments. The formal definition of ontological commitment is given below. For pragmetic reasons, we choose to write an ontology as a set of definitions of formal vocabulary. Although this isn't the only way to specify a conceptualization, it has some nice properties for knowledge sharing among AI software (e.g., semantics independent of reader and context). Practically, an ontological commitment is an agreement to use a vocabulary (i.e., ask queries and make assertions) in a way that is consistent (but not complete) with respect to the theory specified by an ontology. We build agents that commit to ontologies. We design ontologies so we can share knowledge with and among these agents.