"OntoSphere3D is a Protégé plug-in for ontologies navigation and inspection using a 3-dimensional hyper-space where information is presented on a 3D view-port enriched by several visual cues (as the colour or the size of visualized entities)."
While I'm not usually a fan of 3D interfaces this is a fairly intuitive approach. It's certainly seems better than the neighbourhood view and hyperbolic view that they talk about in their paper. They offer a "global view" (projected onto a sphere) and "tree focus".
Java 3D can be pain to install, at least it was for me, as it wouldn't detect Protégé's JRE to install into.