'Instance of' and 'subclass of' provide Wikidata with a way to express the basic philosophical notion of type-token distinction [3]. For things that are a subclass of something like 'material entity', all instances are physical objects that have a unique location in space and time.
Not all instances are spatiotemporal particulars, though. For example, one might say "Homo sapiens instance of taxon", where taxon is a metaclass, i.e. a class in which the instances are classes. (Here 'taxon' would not be a subclass of 'material entity' -- i.e. taxa are information artifacts, not physical objects.) Support for this kind of "punning" via metamodeling is a major feature of OWL 2 DL [4].
If this sort of thing interests you, definitely take a look into Wikidata [5]. The project will be a sea change for several key features in Wikipedia (e.g. infoboxes), and will likely be a main hub of the Semantic Web.
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1. https://www.wikidata.org/wiki/Property:P31
2. https://www.wikidata.org/wiki/Help:Basic_membership_properti...
3. http://plato.stanford.edu/entries/types-tokens/