Increasing numbers of museums and cultural institutions are using 3D laser scanning techniques to preserve cultural artefacts as 3D digital models, that are then accessible to curators, scholars and the general public via Web interfaces to online galleries. Museums are finding the cost of providing metadata for such collections prohibitive and are keen to explore how they might exploit Web 2.0 social tagging and annotation services to capture community knowledge and enrich the contextual metadata associated with their collections. Although there exist some annotation services for 3D objects, they are designed for specific disciplines, not Web-based or depend on proprietary software and formats. The majority also only support the attachment of annotations to whole objects - not points, 3D surface regions or 3D segments. This paper describes the 3DSA (3D Semantic Annotation) system developed at the University of Queensland that enables users to attach annotations to 3D digital artefacts. The 3DSA system is based on a common interoperable annotation model (the Open Annotations Collaboration (OAC) model) and uses ontology-based tags to support further semantic annotation and reasoning. This common approach enables annotations to be re-used, migrated and shared - across annotation clients and across different 3D and 2.5D digital representations of the one cultural artifact. Such interoperability is essential if cultural institutions are to easily harness knowledge from a broad range of users, including curators, students and remote Indigenous communities, with different client capabilities.