Freebase: semantic search, dropdown options clarify search term, snippet description pull out is excellent
V&A: faceted search, advanced search, image & display methods - thumbnail / listing
National Maritime Museum: faceted search, lots of options to refine search, display methods
Rijksmuseum search with sectional dropdown, combined full site search, faceted search
SemanticMuseum is a prototype by Prescient Software (founded Jan 2010).
PHP and JS. Nice demo site with faceted search and semantic links, nice movie.
Polish National Digital Museum aggregates collections from 70 contributing institutions and has 681 thousand objects. Uses RDF, CIDOC CRM, and Europeana-relevant vocabularies. Uses OWLIM as RDF repository