Just to make sure you're aware of this: when mapping classes use owl:equivalentClass and when mapping properties use owl:equivalentProperty. owl:sameAs is for linking individuals, i.e. "instances of classes".
Dan Brickley posted something on vocabulary mapping yesterday which might be interesting in this context.
I rarely declare equivalences between classes or properties when creating ontologies because I figure the best thing to do is to use the external ontology directly. This then leads to the problem of how to declare which other ontologies someone might use together with yours - which is strongly tied to the notion of defining "application profiles" of ontologies.
Sometimes there's also the problem that a complex data structure (several linked resources with certain properties) expressed in one ontology is equivalent to some other structure expressed in some other ontology but you can't easily map this just by declaring equivalences in OWL (because the classes / properties might not be equivalent in every case or aspect). Then it seems like you need rules to do the mapping. I think what we need here is some best practices of how to link such mapping rules to ontologies or just classes.
And as I said, often the best thing to do is to use external identifiers (like UMBEL ones) or ontologies directly rather than creating your own and mapping to something else. Many stores still don't do inferencing so common identifiers or custom rule transformations (like database views) are the only way to do data integration with them.
